Modular antigen transportation molecules and uses thereof in animals

ABSTRACT

The present invention relates to (isolated) recombinant proteins, also referred to as improved MAT (iMAT) molecules, comprising at least one translocation module, at least one targeting module and at least one antigen module, wherein at least one cysteine residue is substituted with a different amino acid residue. Such iMAT molecules are useful specifically as vaccines, e.g. for therapy and/or prevention of allergies and/or infectious diseases and/or prevention of transmission of infectious diseases in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines. The present invention further relates to nucleic acids encoding such iMAT molecules, corresponding vectors and primary cells or cell lines.

SEQUENCE LISTING

This application contains a sequence listing in accordance with 37 C.F.R. 1.821-1.825. The sequence listing accompanying this application is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to (isolated) recombinant proteins, also referred to as improved MAT (iMAT) molecules, comprising at least one translocation module, at least one targeting module and at least one antigen module, wherein at least one cysteine residue is substituted with a different amino acid residue. The iMAT molecules can be produced with substantially reduced manufacturing efforts and are species-specific, safer and immunologically very effective. Such (isolated) recombinant proteins are useful specifically as vaccines, e.g. for therapy and/or prevention of allergies and/or infections and/or prevention of transmission of infections in animals, preferably ruminants, pigs, humans, dogs and/or cats, but excluding equines.

BACKGROUND OF THE INVENTION

Prior art publication from Crameri et al. describes the background in more detail (Crameri R. et al., Allergy 2007, 62: 197-206). Briefly, the processing of antigens by antigen-presenting cells (APCs) takes place by two different routes. Antigens occurring inside the cell are presented by MHC I (major histocompatibility complex class I, MHC class I) molecules on the cell surface, whereas extracellular antigens are presented by MHC II (major histocompatibility complex class II, MHC class II) molecules on the cell surface.

Both mechanisms initiate an immune response by the host to the antigen. Major histocompatibility class-II molecules are cell surface glycoproteins that present peptides to CD4+ T cells. In the endoplasmic reticulum (ER), MHC-II molecules become associated with a type II transmembrane protein termed the invariant chain (Ii) preventing peptide binding to MHC-II in the ER. Ii homotrimers associate in the ER with 3 MHC class II αß dimers and this prevents the binding of endogenous peptides to class II molecules. The N-terminal cytoplasmic domain of Ii contains targeting motifs which leads to its retention in the ER, or to targeting of class II αß dimers into the endosomal-lysosomal pathway via the Golgi. Subsequent proteolytic degradation of Ii leaves a small fragment CLIP (Class II associated Ii peptide) bound to class II αß dimers in the peptide-binding groove. The interaction of class II αß/CLIP complexes with HLA-DM, a class II-related αß dimer, in a specialized compartment releases the CLIP and allows the class II molecules to bind peptides derived from exogenous proteins. It has been shown that endogenously synthesized proteins, generally excluded from the MHC-II presentation pathway, can be efficiently presented as peptide-MHC-II complexes when they are expressed as Ii fusion proteins. This property has been exploited to clone genes encoding MHC-II-restricted antigens from cell lines transfected with Ii-cDNA fusion libraries. Efficient allergy vaccines targeting the MHC-II processing and presentation pathway were achieved using translocable Ii-allergen fusions. The concept, termed modular antigen translocation (MAT) technology bases on a fusion protein consisting of a TAT-derived translocation peptide converting extracellular into cytoplasmic proteins, the first 110 amino-acids of Ii for targeting the fusion proteins to endosomal/lysosomal compartments, and an antigen for induction of specific immune responses.

The concept of providing modular antigen transportation (MAT) molecules for modulating immune responses, associated constructs, method and uses thereof is disclosed in WO 2004/035793 (US equivalent US 2005/0281816). This document describes the usefulness of a three-part-molecule, the MAT molecule, for introducing epitopes of antigens into cells, thus, determining the immune response to be modulated by such MAT molecule. Therein, various translocation modules, targeting modules as well as antigen modules are described. This technology and its underlying method make it possible, firstly, to convey antigens efficiently from the extracellular space into the intracellular space of a target cell, and, secondly, make it possible for the antigens, after arrival in the interior of the cell, to reach efficiently cell organelles in order to be subsequently processed for antigen presentation. Generally, the two-stage process can be utilized for the targeted, efficient modulation of the immune response in a subject. The use of MAT molecules is disclosed for example in Martinez-Gómez J M et al. [Allergy 2009, 64(1): 172-178]; Rose H (Arb Paul Ehrlich Inst Bundesinstitut Impfstoffe Biomed Arzneim Langen Hess, 2009, 96, 319-327) as well as recently in Senti G et al. [J Allergy Clin Immunol., 2012, 129(5): 1290-1296]. Based on the MAT technology, the major cat allergen Fel d1 was fused to a TAT-derived protein translocation domain and to a truncated invariant human chain for targeting the MHC class II pathway. Immunogenicity was evaluated in mice, while potential safety issues were assessed by suitable tests based on basophil reactivities from cat-dander-allergic patients. The possible use of this model compound has been demonstrated. It is described therein, that it is expected that MAT molecules are safer and more efficient in inducing the desired immune response, namely hyposensitization, than recombinant allergens or allergen extracts in conventional allergen-specific immunotherapy (SIT). In the recent publication by Senti G. et al. intralymphatic immunotherapy for cat dander allergy in humans inducing tolerance after three injections was described. Therein, a first-in-human clinical study with the MAT-Fel d1 was described, demonstrating safety and induction of allergen tolerance after intralymphatic injection of three injections, only.

Further prior art is as follows:

Gadermaier G et al. (Molecular Immunology 2010, 47: 1292-1298) described the targeting of the cysteine-stabilized fold of Art v1 for immunotherapy of Artemisia pollen allergy. The authors used genetic engineering approaches for targeting Art v1 posttranslational modifications aiming at the creation of hypoallergenic molecules: (i) disulfide bridges of the defensin domain were disrupted by site-directed mutagenesis and (ii) the mutant constructs expressed in E. coli for the production of non-glycosylated proteins. However, the objective was clearly only manipulating the three-dimensional fold of the Art v1 defensin domain to abrogate IgE-binding (i.e. creating a hypoallergenic molecule) by exchanging single cysteine residues for serine—while keeping intact (i.e. unmodified) the recognized T-cell epitopes (even if such contain cysteine residues).

The report of the 3^(rd) Havemeyer workshop on allergenic diseases of the Horse (Hólar, Iceland, June 2007, Veterinary Immunology and Immunotherapy 2008, 126: 351-361) focused on immunological and genetic aspects of insect's bite hypersensitivity (IBH) and recurrent airway obstruction (RAO). At this workshop novel approaches for SIT against IBH were discussed, among others the use of viral vectors or protein vaccination with allergens coupled to modular antigen translocating (MAT) molecules.

In SIAF Annual Reports 2010 and 2011 Crameri R reports the use of MAT technology for vaccination of IBH-affected horses.

Zhao et al. (Int J Clin Exp Med 2015; 8(4):6436-6443) reported results of experiments with mosaic fusion proteins with the MAT structure disclosed in WO 2004/035793 and 3 segments of T cell epitope coding for Der p1 as antigen module. They reassembled these sequences in linear manner to form a fusion gene for protein expression. They describe their construct to exhibit a stronger allergenicity (hyperallergenicity) as compared to the Der p1 protein.

However, major problems arose when producing and manufacturing the MAT molecules described in the prior art. In particular standard methods used in developing a downstream process (DSP) for manufacturing of the MAT molecules under good manufacturing practice (GMP) could not be applied. It was not possible to purify a homogeneous molecular species of the MAT molecules, evidently due to their anomalous physicochemical properties.

Several methods of purification could not be applied (see Example 4 herein) with the MAT molecules described in the prior art although different separation principles (e.g., size exclusion chromatography, RP-HPLC) were tested. Methods applied for determination of purity for recombinant proteins in general include chromatographic separation, e.g. RP-HPLC and electrophoretic separation (e.g. capillary zone electrophoresis, isoelectric focusing, SDS-PAGE under reducing or non-reducing conditions). Also, these analytical methods could not be applied on MAT molecules without molecule-specific adaptations. For the assessment of purity, an adapted specific SDS-PAGE test procedure had to be developed. This test procedure includes sample preparation with reducing agent and lithium dodecyl sulfate (LDS) and heating up to 75° C., resulting in multiple, reproducible sharp bands after electrophoretic separation. Staining with Coomassie blue dye leads to linear quantitative behavior (densitometry) in gels. Using a monoclonal antibody that allows for detection of the allergen module in a MAT molecule exhibited a main band and several minor bands. All bands migrate reproducibly to the same position as in the original gel also after re-loading a second gel with excised bands of the first gel. Surprisingly, in all of these bands with apparent lower and higher molecular weight, the full length MAT molecules were identified by excision of bands out of the gel, their tryptic digestion and subsequent analysis by mass spectrometry (nanoLC/ESI-MS-MS). From these experiments an untypical, anomalous behavior of different folding variants of MAT molecules in the SDS-PAGE can be concluded (“gel shifting”). Furthermore, in all batches of MAT molecules multimeric forms of the protein could be detected which were difficult to separate from monomeric forms.

For e.g. economic aspects, but also for regulatory requirements, it is necessary to improve (i) the manufacturing process of the MAT molecules and (ii) their suitability for standard analytical methods of purity determination. Additionally, for adapting the MAT molecules to specific target species, such as ruminants, pigs, dogs and/or cats, adaption of the immunological targeting within the MAT technology is required. This species specificity is necessary to be represented in said iMAT molecules since differences in homologues Ii amino acid sequences between mammalian species exist (FIG. 10). However, a proper binding of the Ii fusion protein (iMAT) to the αß subunits of MHC class II, specifically in the CLIP region is required for an optimal immunological function with respect to the antigen in said iMAT molecules. A proper binding to said MHC class II molecules is achieved if the Ii sequence in iMAT does resemble the original as far as possible.

Additionally, the MAT molecules are readily employed in allergies elicited by a known major allergen (e.g. cat dander allergy in humans by Fel d1). However, it seems difficult to employ the MAT molecules of the prior art in clinical settings, such as allergies, where for instance a variety of non-cross-reactive allergens are known to be involved, but the importance of such allergens in eliciting the allergy is unknown (i.e. the major allergens are unknown).

Furthermore, the prior art does not describe how more than one (e.g. 2, 3, 4 or more) allergen can be embedded into (i)MAT molecules without exceeding a certain size of the fusion protein that hinders protein manufacturing.

The objective underlying the invention is to provide improved MAT molecules useful as active agents in pharmaceutical composition, such as vaccines, and their corresponding therapeutic and/or preventive uses in animals, excluding equines, which overcome the problems of the prior art.

SUMMARY OF THE INVENTION

In one aspect, the objective underlying the invention has surprisingly been solved by providing a(n) (isolated) recombinant protein, preferably an improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells,

(ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, preferably processed antigens, and

(iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial epitope of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such iMAT molecule,

characterized in that at least in the antigen module(s) at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid, for use in a method of prevention and/or therapy of one or more allergies in animals excluding equines and/or for use in a method of prevention and/or therapy of one or more infectious diseases in animals excluding equines and/or for use in a method of prevention of transmission of one or more infectious diseases in animals excluding equines and/or for use in a method of prevention of transmission of one or more infectious diseases in animals excluding equines by vectors.

Corresponding methods of prevention and/or treatment of animals excluding equines, in need thereof and uses for the preparation of a pharmaceutical composition/medicament for the prevention and/or treatment of animals excluding equines, are also intended to be within the scope of the present invention.

Preferably, in the at least one antigen module all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. More preferably in the entire iMAT molecule all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

Preferably, if not all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid, an even number of cysteine residues remains in the entire iMAT molecule.

Preferably, all of such modules are covalently linked to each other, optionally by additional spacer module(s) between two or more adjacent, optionally all, of such first, second and/or third modules.

More preferably, all of such modules are covalently linked to each other and no additional spacer module(s) are present between two or more adjacent modules of such first, second and/or third modules at all.

In another aspect, the objective underlying the invention has surprisingly been solved by providing an iMAT molecule relating to one or more of the amino acid sequences according to SEQ ID NOs:2 or 3, preferably comprising one or more of the amino acid sequences according to SEQ ID NOs:4 or 5. In a further aspect, the objective underlying the invention has surprisingly been solved by providing an iMAT molecule comprising one or more of the amino acid sequences according to SEQ ID NOs:14-23. In a preferred aspect, the objective underlying the invention has surprisingly been solved by providing an iMAT molecule comprising, preferably consisting of, one or more of the amino acid sequences according to SEQ ID NOs: 24-83.

In another aspect, the objective underlying the invention has surprisingly been solved by providing a vaccine or immunogenic composition or pharmaceutical composition comprising the (isolated) recombinant protein as herein disclosed and claimed.

In another aspect, the objective underlying the invention has surprisingly been solved by providing the (isolated) recombinant protein as herein disclosed and claimed or the vaccine or immunogenic composition or pharmaceutical composition as herein disclosed and claimed for use in a method of prevention and/or therapy of one or more allergies in animals, preferably dogs and/or cats, but excluding equines; preferably allergies to flea bites preferably in dogs and/or cats; allergies to certain food components preferably in dogs and/or cats; atopic dermatitis preferably in dogs and/or cats; allergic airway inflammation and/or obstruction preferably in cats. Corresponding methods of prevention and/or treatment of animals, preferably dogs and/or cats, but excluding equines, in need thereof and uses for the preparation of a pharmaceutical composition/medicament for the prevention and/or treatment of animals, preferably dogs and/or cats, but excluding equines, are also intended to be within the scope of the present invention.

In another aspect, the objective underlying the invention has surprisingly been solved by providing the (isolated) recombinant protein as herein disclosed and claimed or the vaccine or immunogenic composition or pharmaceutical composition as herein disclosed and claimed for use in a method of prevention and/or therapy of one or more infectious diseases in animals, preferably ruminants, pigs, dogs and/or cats, but excluding equines, and/or prevention of transmission of one or more infectious diseases in animals, preferably ruminants, pigs, dogs and/or cats, but excluding equines, by vectors, preferably by blood feeding bugs, flies, midges, ticks and/or mosquitos. The infectious pathogen and/or infectious disease may be one or more selected from Campylobacter, heartworm, ehrlichiosis, leishmaniosis, trypanomiasis, borreliosis, Schmallenberg-, blue tongue- and/or west nile virus infection, dermatophytosis and/or infections of the digestive tract and/or other organs by viruses (e.g. rota-, coronavirus) and/or parasites (e.g., helminths) and/or protozoa (e.g., coccidiosis, cryptosporidiosis) and/or their pre-patent stages. Corresponding methods of prevention and/or treatment of animals, preferably ruminants, pigs, humans, dogs and/or cats, but excluding equines, in need thereof and uses for the preparation of a pharmaceutical composition/medicament for the prevention and/or treatment of animals, preferably ruminants, pigs, humans, dogs and/or cats, but excluding equines, are also intended to be within the scope of the present invention.

In a further aspect, the objective underlying the invention has surprisingly been solved by providing a nucleic acid encoding the (isolated) recombinant protein as herein disclosed and claimed.

In a further aspect, the objective underlying the invention has surprisingly been solved by providing a vector comprising at least one nucleic acid as herein disclosed and claimed.

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing a primary cell or cell line comprising at least one nucleic acid as herein disclosed and claimed and/or at least one vector as herein disclosed and claimed.

Surprisingly, the iMAT molecules according to the present invention, as herein disclosed and claimed, do possess physicochemical and/or immunological characteristics that render them superior to the MAT molecules of the pertinent prior art:

(i) The substitution of at least one cysteine residue, preferably all cysteine residues, with a different amino acid residue in the antigen module(s), preferably entire iMAT molecule, which was selected in silico not to compromise the stability of the final iMAT molecule, renders the iMAT molecule according to the present invention surprisingly suitable for the application of standard purification procedures for biopharmaceuticals as well as for standard analytical methods.

(ii) The preferred direct covalent linkage of the modules of the iMAT molecule, i.e. first translocation module, second targeting module and third antigen module, without any additional spacer modules between such modules, i.e. no additional spacer modules between two or more adjacent modules of such first, second and/or third modules at all, contributes in addition to the superior characteristics of the iMAT molecules according to the present invention: such iMAT molecules which are thought to be more rigid in three-dimensional structure and hence unable to form conformational IgE epitopes, are even more hypoallergenic—virtually to the extent of no allergenicity at all.

(iii) The preferred presence of a(n) (quasi) N-terminal or C-terminal His-tag results in iMAT molecules according to the present invention that can be used as a surrogate marker for monitoring immunity and/or duration of immunity since such tag module, optionally together with one or more adjacent amino acid residues from the translocation module, can be used to induce a specific immunologically detectable signal (e.g. an antibody) in the target subject, that is specific to the structure of the iMAT molecules (see Example 1 herein). Additionally, the presence of such tag module can be used for separating proteins in a sample containing the iMAT molecules according to the present invention, e.g. using zinc- or cobalt-charged solid supports, and hence further improves the possibility to produce iMAT molecules according to the present invention without aggregation during the purification process. A(n) (quasi) N-terminal His-tag is preferred.

(iv) The at least one targeting module in the iMAT molecules according to the present invention is preferably species-specific, i.e. in case of an intended application of such iMAT molecules to canine, feline, bovine, ovine, caprine or porcine a targeting module, e.g. the canine invariant chain, is chosen accordingly. By this species-specific targeting optimized binding characteristics of the iMAT molecules according to the present invention to the MHC Class II molecules can successfully be achieved.

(v) The at least one antigen module in the iMAT molecules according to the present invention is preferably an allergen. This could be derived from food and/or mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces) and/or fleas, preferably pollen from tree, grass, herbaceous, Ambrosia and/or brassicaceae pollen and/or fungi and/or their spores of the genera Aspergillus, Alternaria, Botrytis, Cercospora, Cladosporium, Curvularia, Drechslera, Eurotium, Helminthosporium, Epicoccum, Erysipheloidium, Fusarium, Lichtheimia, Nigrospora, Penicillium, Periconia, Peronospora, Polythrincium, Saccharopolyspora (formerly also Faenia or Micropolyspora), Thermoactinomyces, Stemphylium, torula and/or mites (or their feces) of the genera Acarus, Glycophagus, Tyrophagus, Dermatophagoides, Euroglyphus, Lepidoglyphus, Blomia and/or fleas of the genera Ceratophyllus, Ctenocephalides, Pulex, Archaeopsylla. The at least one antigen module in the iMAT molecules according to the present invention is more preferably a Dermatophagoides allergen. The allergen can be selected according to the following criteria: when major allergens eliciting an allergy in subjects are unknown, the at least one antigen module in the iMAT molecules according to the present invention can be selected by a bioinformatics approach as described exemplarily and in detail in Examples 5 and 6 herein. By this means improved MAT molecules can be achieved which are useful specifically as vaccines, e.g. for therapy and/or prevention of allergies in animals, preferably dogs and/or cats, but excluding equines. The at least one antigen module in the iMAT molecules according to the present invention may also be an antigen of a pathogen involved in one or more infectious disease(s). This could be derived from the genera Campylobacter, Dirofilaria, Ehrlichia, Leishmania, Trypanosoma, Borrelia, Orthobunyavirus, Orbivirus, Flavivirus, Rotavirus, Coronavirus, Trichophyton, Microsporum; other helminths like Cooperia, Haemonchus, Ostertagia, Trichostrongylus, Dictyocaulus, Metastrongylus; and/or protozoa with gastrointestinal infestation like Eimeria, Isospora, Cryptosporidium, Giardia—in case of parasites also antigens derived of the pre-patent stages might be employed. The at least one antigen module in the iMAT molecules according to the present invention may also be an antigen (e.g. saliva component) of a vector involved in the transmission of one or more infectious disease(s), e.g., belonging to the families Culicidae, Ceratopogonidae, Phlebotominae Ixodidae and/or Cimicidae. By this means improved MAT molecules can be achieved which are useful specifically as vaccines, e.g. for therapy and/or prevention and/or prevention of transmission of infectious diseases in animals, preferably ruminants, pigs, dogs and/or cats, but excluding equines.

(vi) Production of novel iMAT molecules that comprise sequence motifs of more than one allergen in only one of said iMAT molecule, i.e. mosaic fusion proteins, can be achieved. The selection of the peptide sequences embedded in the allergen module is based on pan allergenic motifs detected in the relevant major allergens by bioinformatics tools. By this approach the size of such iMAT molecules can be kept low enough to allow efficient production in suitable expression systems.

In particular, the present invention provides (isolated) recombinant proteins exhibiting an improved solubility, that are readily applicable to chromatographic separation techniques and that show an improved stability.

In addition, the (isolated) recombinant proteins according to the present invention preferably display high activities and efficacies in inducing the desired immunological effects, namely, advantageously species specific modulating the immune response against allergens in a subject becomes feasible, e.g. in animals, more preferably dogs and/or cats, but excluding equines, allergen specific IgE mediated hypersensitivity reactions may be modulated in different target organs as skin, respiratory and/or the gastrointestinal system. And/or prevention and/or therapy of infectious diseases and/or prevention of transmission of infectious diseases by vectors in animals, preferably ruminants, pigs, humans, dogs and/or cats, but excluding equines, becomes feasible.

The allergenicity of a therapeutic allergen is of utmost importance, it is a measure of the potential to induce adverse events, e.g. provoke anaphylaxis. With regard to prior art MAT molecules conflicting results about their allergenicity in comparison to the corresponding native allergens have been reported in the prior art. Senti G et al. (J Allergy Clin Immunol. 2012, 129(5): 1290-1296) demonstrated hypoallergenicity of a MAT-Fel d1 in the Cellular Antigen Stimulation Test (CAST) assay as well as in the intradermal and in the intracutaneous test. The quantitative difference in sensitivity between the allergen and the MAT molecule comprising the Fel d1 was 100-, 23- and 16-fold, respectively. Though MAT-Fel d1 was clearly hypoallergenic, some allergenicity remained. In contrast Zhao et al. (Int J Clin Exp Med 2015; 8(4): 6436-6443) describe their MAT-Der p1 construct to exhibit an even stronger allergenicity (hyperallergenicity) as compared to the native Der p1 protein.

Surprisingly, the safety of the improved MAT molecules, as disclosed and claimed herein, is superior in this respect. In contrast to native allergens, which usually elicit a strong histamine release, surprisingly the iMAT molecules according to the present invention show virtually no histamine release response at all. Thus, iMAT molecules show superiority in respect to safety as compared with the MAT molecule as described in the prior art (see above).

The consequence of this surprising safety property of iMAT molecules in contrast to prior art MAT molecules is, that iMAT molecules used as desensitizing proteins can be used similar to vaccines against pathogens. No up-dosing as with classical therapeutic allergens is needed, since vaccines comprising iMAT molecules do not show allergen properties with respect to allergic adverse events. Already the dose of the first injection of the iMAT molecule in a treatment course is selected based on efficacy considerations only and one does not have to consider potential allergic adverse reactions. This could not be performed using MAT molecules described in the prior art since the allergenicity of MAT, compared to the native allergen, is only reduced to a certain level. However, MAT molecules described in the prior art are still allergens; iMAT molecules in contrast are not. The advantage of this improved property renders a more efficacious treatment regime possible with e.g. three subcutaneous or intralymphatic injections with a high biopharmaceutical content (e.g. 3 times 1 μg to 100 μg, preferably 3 times 10 μg to 50 μg iMAT protein).

The lack of allergenicity of the iMAT molecules can be explained by the fact that in contrast to the MAT molecules described in the prior art no linker amino acid residues [i.e. spacer module(s) between the first, second and/or third module(s)] are used to separate the different modules in such iMAT molecules.

It is known in the prior art that engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker, such linker is important for the function (e.g. epitope recognition by the immune system) of the proteins [Klein J S et al., Protein Eng Des Sel. 2014, 27(10): 325-330]. The separation distance between functional units can impact epitope access and the ability to bind with avidity.

It is assumed that in iMAT molecules of the present invention, which are missing the amino acid residue linkers between the modules, in particular between the targeting domain and the antigen module, lead to a more rigid structure, conformational epitopes of the allergen module might not be formed due to incorrect folding. A cross linking of antibodies bound on the surface of basophils (e.g. IgE) by its high affinity receptors is necessary to induce activation and histamine release. However, misfolded allergens might not be able to induce such cross linking. Thus, an iMAT molecule without additional spacer modules/linkers between the first, second and third module may not form conformational IgE epitopes, which renders the iMAT molecules according to the present invention non-allergenic. Thus, in a specific embodiment the iMAT molecules of the present invention lack any additional spacer modules or linkers between the first, second and third module.

DETAILED DESCRIPTION OF THE INVENTION

Before the embodiments of the present invention are described in further details it shall be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. All given ranges and values may vary by 1 to 5% unless indicated otherwise or known otherwise by the person skilled in the art, therefore, the term “about” was usually omitted from the description and claims. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing the substances, excipients, carriers, and methodologies as reported in the publications which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

The terms “isolated recombinant protein”, “recombinant protein” and/or “improved MAT (iMAT) molecule” are interchangeably used in the course of the present invention. They all have the identical meaning.

The term “module” in the course of the present invention refers to a specific amino acid sequence, e.g. a part, a unit or a moiety of a polypeptide, usually short amino acid/peptide sequences, having a defined function.

The term “first module being an amino acid sequence allowing the translocation of the (isolated) recombinant protein, preferably improved MAT (iMAT) molecule, from the extracellular space into the interior of cells”, herein also interchangeably referred to as “translocation module” or “translocation sequence”, in the course of the present invention refers to a specific amino acid sequence that promotes the transport of the cargo molecule, e.g. amino acid sequence, peptide, polypeptide, protein and other classes of substances, such as nucleic acids or pharmaceutically active ingredients (API), to the interior of cells, in particular eukaryotic cells, more particular, cells expressing the MHC class II molecules on the surface and/or the MHC class I molecules on the surface, as known in the literature.

By the presence of the translocation module it is possible to promote the entry of said cargo molecule into the cells.

Amino acid sequences useful as translocation modules are described in the prior art. For example, U.S. Pat. No. 7,653,866 discloses several useful translocation sequences including the HIV-tat molecule or the protein VP22, which is derived from herpes simplex virus. This principal of promoting the entry of a given target molecule into the interior of cells is described numerously in various studies in the pertinent patent and non-patent literature. In addition, suitable translocation sequences include homeoprotein sequences, leucine zipper sequences, arginine-rich and/or lysine-rich sequences, and various other sequences of proteins or polypeptides which are secreted despite the absence of a secretion signal sequence. Particularly useful are viral peptide sequences, e.g. the protein HIV transcriptional activator protein (HIV tat). The Tat sequence or Tat peptide has been described in the prior art including various modifications. All the variations described in the prior art for peptide sequences of Tat are generally suitable as translocation modules. Other examples include the VP22 peptide as well as antennapedia peptides derived from the Drosophila homeotic protein antennapedia. In addition, other homeoproteins may be used. Various examples of suitable homeoproteins are described in the prior art. In addition, leucine zipper proteins, like human cFos-(139-164), or human cJun-(252-279) can be used. Moreover, arginine-rich and/or lysine-rich peptides are suitable as translocation modules including sequences like HIV-1 rev (34-50) or other peptides derived from virus or yeast. Of course, the polyarginine-rich and/or polylysine-rich peptides can be produced synthetically. Said polyarginine-rich and/or polylysine-rich peptides may comprise further amino acids. Suitable examples are described in the pertinent prior art.

In a preferred embodiment, the at least one translocation module comprises, preferably consists of, an amino acid sequence which does not consist of a complete protein sequence, as illustrated above, but instead of a minimal sequence still being functional, i.e. capable of effectively promoting cell entry. A suitable minimal sequence is for instance the amino acid sequence YGRKKRRQRRR (SEQ ID NO: 1).

In another preferred embodiment, the at least one translocation module comprises, preferably consists of, HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof, provided that such at least one translocation module is functional as a module for translocation from the extracellular space into the interior of cells.

The term “second module being an amino acid sequence allowing species-specific intracellular targeting of the (isolated) recombinant protein, preferably improved MAT (iMAT) molecule, to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, preferably processed antigens”, herein also interchangeably referred to as “targeting module” or “targeting sequence”, in the course of the present invention refers to a specific amino acid sequence that allows/promotes the intracellular transport of the (isolated) recombinant proteins, as disclosed and claimed herein, to such cell organelles that are involved in the processing of antigens and/or the loading of MHC molecules with antigens.

In particular, such cell organelles include the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, lysosomes, endosomes and MHC II compartments. These intracellular organelles are involved in processes such as, for example, the transport and/or processing of antigens, the preparation and/or loading of MHC II molecules with antigens or processed antigens, and/or the transport of the MHC II molecules loaded with such antigens to the cell surface.

A number of sequences are known in the prior art. A prominent example of useful targeting sequences includes the invariant chain of MHC class II molecules also known as Ii invariant chain or MHC II gamma chain. Various variants of the invariant chain are described in the patent and non-patent literature.

In a preferred embodiment of the present invention, the invariant chain is chosen from the species in which the immune response should be modulated and/or from the species in which the iMAT molecule should be intracellularly targeted. This species specificity is necessary to be represented in said iMAT molecules since differences in homologues Ii amino acid sequences between mammalian species exist (FIG. 10). However, a proper binding of the Ii fusion protein (iMAT) to the αß subunits of MHC class II, specifically in the CLIP region is required for an optimal immunological function with respect to the antigen in said iMAT molecules. A proper binding to said MHC class II molecules is achieved if the Ii sequence in iMAT does resemble the original as much as possible.

For example, for dogs, cats, cattle, sheep, goats or pigs the preferred invariant chain chosen is the canine, feline, bovine, ovine, caprine or porcine invariant chain. For dogs and cats, the preferred invariant chain is the amino acid sequence according to SEQ ID NO: 2 (canine) and SEQ ID NO: 3 (feline) or fragments thereof, provided such fragments maintain their intracellular transport function (e.g. the first 110 amino acids as shown in FIG. 10).

Other suitable examples for targeting sequences include lysosomal membrane proteins, comprising sequences suitable as targeting modules. That are, a number of membrane proteins occurring in lysosomes which have sequence motifs that allow targeting the lysosome. These groups of proteins include inter alia lamp 1, lamp 2, lamp 3, limp II and lap. In addition, tetraspan proteins are known in the prior art as targeting modules. Additional proteins can be found in the endosomal/lysomal compartments that show targeting properties. A skilled person is aware how to determine suitable targeting sequences accordingly.

In another embodiment, the at least one targeting module comprises, preferably consists of, the canine, feline, bovine, ovine, caprine or porcine invariant chain or fragments thereof provided such fragments maintain their intracellular transport function.

In a preferred embodiment, the at least one targeting module is the canine invariant chain, comprising, preferably consisting of SEQ ID NO: 4 (canine).

In a further preferred embodiment, the at least one targeting module is the feline invariant chain, comprising, preferably consisting of SEQ ID NO: 5 (feline).

The term “third module as antigen module being an amino acid sequence derived from at least one full or partial epitope of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such (isolated) recombinant protein, preferably improved MAT (iMAT) molecule (in a subject, preferably an animal, more preferably a ruminant, pig, dog and/or cat, but excluding an equine)”, herein also interchangeably referred to as “antigen module” or “antigen sequence”, in the course of the present invention refers to a specific amino acid sequence that allows modulating the immune response against the epitope/antigen and determining the specificity of the immune response in a subject, preferably an animal, more preferably a ruminant, pig, dog and/or cat, but excluding an equine.

In this context, such antigen module(s) comprise(s) at least one cysteine residue that is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. Thus, the immune response is different compared to the immune response of a subject, preferably an animal, more preferably a ruminant, pig, dog and/or cat, but excluding an equine, exposed to the unchanged amino acid sequence of the antigen.

There are no restrictions relating to the antigens on the basis of the method. The method can be used for example for activating the immune system of a subject against pathogens such as, for example, against viruses, bacteria, fungi, parasites, protozoa etc., i.e. very generally as vaccine. Additionally, the method can be used not only directly against such pathogens, but also to activate the host immune system to prevent the transmission in vector-borne diseases involving viruses, bacteria, fungi, parasites, protozoa, etc. In addition, the method can be used to activate the immune system against degenerated cells such as, for example, tumor cells, etc. However, it can also be used on the other hand for desensitization of the immune system of a subject against allergens such as, for example derived from food and/or aeroallergens, e.g. mold (fungi and/or their spores), pollen, animal hair, house dust or forage mites (and/or their feces), insect toxins, etc. or for targeted suppression of the immune system, e.g. if autoimmune reactions are present, such as, for example, arthritis, rheumatism, diabetes, SLE (systemic lupus erythematosus), etc., and for suppressing transplant rejection reactions. Further disorders which are not expressly mentioned and which are associated with an immune reaction which is too strong or too weak can likewise be treated with the iMAT molecules, as disclosed and claimed herein.

It is possible to employ as antigen modules for the purposes of the invention in principle all types of antigens able to modulate an immune response. Both, antigens currently already known and antigens to be discovered in future are suitable. In some circumstances, the antigens may also be those which do not lead to an immune response with conventional immunization methods known in the art at present, but which lead on application of the novel method described in the present invention to an immune response by the subject. Further, the term antigen encompasses antigenic fragments comprising the antigenic determinant/the antigenic determinants which are also known as epitope(s). Thus, the antigen module may be the whole molecule, e.g. the protein, or is a part of the molecule, i.e. a fragment thereof, like a peptide, encompassing at least one antigenic determinant or epitope. The at least one antigenic determinant or epitope is able to elicit an immune response against the antigen. The epitope can comprise one or more than one amino acid or peptide or other structure capable of eliciting an immune response such as sugar structures, phosphorylated amino acids, etc. or combinations thereof. The antigen can be a continuous epitope (i.e. not dependent on conformation, e.g. present in for example native and denatured proteins) or a discontinuous epitope (i.e. dependent on conformation, e.g. only present in native, folded, but not present in denatured proteins). It is possible to use not only proteins and peptides, but also sugar structures, lipids, e.g. lipopolysaccharides, lipoteichoic acids and other constituents of bacterial membranes (CD1b binds, for example, sugar structures and lipids), nucleic acids such as, for example, DNA comprising CpG motifs, organic substances such as, for example, latex or pharmaceutically active substances as antigen for the purposes of the present invention. The antigen may be derived from all possible life forms, such as e.g. animals, plants, fungi, parasites, unicellular or multicellular microorganisms, viruses and other life forms. The antigens may have been isolated from biological material, have been prepared as recombinant antigens or have been prepared by synthesis, e.g. by peptide synthesis. Synthetically prepared antigens may be substances which occur in nature or which do not occur in nature but are obtainable by chemical synthesis. Examples of non-naturally occurring substances which are, however, suitable as antigen in some circumstances are, for example, synthetically prepared substances which are present in medicaments, or synthetic peptides having amino acid sequences which do not occur in nature, or peptidomimetics, etc. Naturally occurring or synthetic or recombinant antigens can be modified by molecular biology, enzymatic, chemical and/or other methods in order to confer on them properties which are more advantageous for the particular application. These advantageous properties may be, inter alia, a higher or lower activity as antigen, a broader or a more specific action as antigen, a better solubility in hydrophilic or hydrophobic solvents, a greater permeability of the antigen modules for cell membranes, for membranes of organelles, for the blood-brain barrier, for the blood-CSF barrier etc., a higher or lower half-life in vivo or in vitro, a lower or higher toxicity, a better detectability of the antigen in vivo or in vitro after application of the antigen in the form of an iMAT molecule etc. It is additionally possible for the purposes of the present invention to combine a plurality of antigens in one antigen module. For this it is possible for identical antigens to be present in more than one copy in the antigen module, or it is possible for example for different variants of the same antigen to be combined in an antigen module. Combination of antigens, e.g. of antigen 1, and other antigens, e.g. of antigen 2, in an antigen module is also possible, etc. Further combinations, such as, for example, antigen 1 in more than one copy and antigen 2 in a single copy may also be combined in an antigen module, etc. It is additionally possible also for one or more different and/or one or more identical antigen modules to be present in an iMAT molecule. In principle, it is conceivable that for all possible combinations of single or multiple, identical or altered, copies of antigens derived from one or more different antigens can be combined for the purposes of the invention.

In a preferred embodiment, the antigen module comprises at least one full or partial epitope derived from at least one antigen, wherein such antigen is an allergen. At least one epitope is able to elicit an immune response against the allergen whereby the epitope can comprise one or more than one structure, e.g. a peptide, capable of eliciting an immune response. The epitope may be a continuous epitope or a discontinuous epitope of the allergen. Epitopes are preferably at least eight amino acids in length preferably are at least ten amino acids in length, more preferably are at least 13 amino acids in length. The antigen module comprises at least one full or partial epitope, but may also comprise two or more full or partial epitopes which may be identical or different from each other. Furthermore, the antigen module may comprise additional amino acid sequences adjacent to the at least one full or partial epitope. The epitope may be the natural occurring epitope or may be a modified epitope, either modified in its amino acid sequence and/or by one or more post-translational modifications.

In an embodiment, the at least one (third) antigen module comprises at least one full or partial epitope derived from at least one antigen of a pathogen involved in one or more infectious disease(s) of animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines. This could be derived from the genera Campylobacter, Dirofilaria, Ehrlichia, Leishmania, Trypanosoma, Borrelia, Orthobunyavirus, Orbivirus, Flavivirus, Rotavirus, Coronavirus, Trichophyton, Microsporum; other helminths like Cooperia, Haemonchus, Ostertagia, Trichostrongylus, Dictyocaulus, Metastrongylus; and/or protozoa with gastrointestinal infestation like Eimeria, Isospora, Cryptosporidium, Giardia—in case of parasites also antigens derived of the pre-patent stages might be employed. The at least one antigen module in the iMAT molecules according to the present invention may also be an antigen (e.g. saliva component) of a vector involved in the transmission of one or more infectious disease(s), e.g. belonging to the families Culicidae, Ceratopogonidae, Phlebotominae, Ixodidae and/or Cimicidae.

In a further preferred embodiment, the at least one (third) antigen module comprises at least one full or partial epitope derived from at least one allergen eliciting one or more allergies in animals, more preferably dogs and/or cats, but excluding equines. This could be at least one full or partial epitope of at least one allergen derived from food and/or mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces), preferably pollen from tree, grass, herbaceous, Ambrosia and/or brassicaceae pollen and/or fungi and/or there spores of the genera Aspergillus, Alternaria, Botrytis, Cercospora, Cladosporium, Curvularia, Drechslera, Eurotium, Helminthosporium, Epicoccum, Erysipheloidium, Fusarium, Lichtheimia, Nigrospora, Penicillium, Periconia, Peronospora, Polythrincium, Saccharopolyspora (formerly also Faenia or Micropolyspora), Thermoactinomyces, Stemphylium, torula and/or mites (or their feces) of the genera Acarus, Glycophagus, Tyrophagus, Dermatophagoides, Euroglyphus, Lepidoglyphus, Blomia and/or fleas of the genera Ceratophyllus, Ctenocephalides, Pulex, Archaeopsylla.

In a preferred embodiment this is, preferably at least one full or partial epitope of at least one allergen derived from mites more preferably from the genus Dermatophagoides.

Examples of allergens of the genus Dermatophagoides are shown in FIG. 9 (9A and 9B) identifying the species, the allergen and the UNIPROT accession number.

In a further preferred embodiment, such at least one allergen is Der f 15 according to SEQ ID NO: 11 (full) and SEQ ID NO: 18 (iMAT form). Preferred specific sequences of the antigen modules are the amino acid sequences according to SEQ ID NOS: 7-23, preferably SEQ ID NOs: 14-23 (iMAT forms).

The term “immune response modulated by” or interchangeably “immunomodulatory immune response”, in connection with “(isolated) recombinant protein” and/or “iMAT molecule” in the course of the present invention refers to immunogenic and/or tolerogenic immune responses.

The term “hybrid iMAT” or “iMAT hybrid” or “mosaic-like iMAT” are used interchangeably. These terms refer to an iMAT molecule, which comprises in its third module more than one full or partial epitope sequence from two or more antigens. Preferably said antigens are two or more allergens, more preferably two or more short peptide sequences from different allergens, determining the specificity of an immune response modulated by such iMAT molecule (in a subject, preferably an animal).

The term “allergen” in the course of the present invention refers to a type of antigen that in the native form produces an abnormally vigorous immune response in which the immune system fights off all perceived threats that would otherwise be harmless to the subject. Typically, these kinds of reactions result in the phenotype known as allergy. Various types of allergens are described in the prior art, including foods, drugs, animal products or natural or synthetic materials. Preferably, a protein is considered to be an allergen, when it elicits in its native form a specific IgE response in at least five subjects, preferably animals, more preferably dogs and/or cats, but excluding equines. For the avoidance of doubt, an “allergen” in connection with the “at least one (third) antigen module comprising at least one full or partial epitope derived from at least one allergen” does not need to be in the native form any longer, which is also preferred—in other words, the term “allergen” in the course of the present invention also explicitly refers to non-native amino acid sequences as part of the iMAT molecules, as described and claimed herein, that do not elicit a specific IgE response in at least five subjects, preferably animals, more preferably dogs and/or cats, but excluding equines, any longer.

The term “allergenicity” of a therapeutic allergen is a measure of the potential to induce adverse events, e.g. provoke anaphylaxis. Exemplarily for an allergy in mammals, an assay to measure allergenicity in dogs is described in Griffin et al. [Griffin C E. Diagnosis of canine atopic dermatitis DOI: 10.1002/9781118738818.ch10]. This document describes measurement of allergen specific IgE mediated hypersensitivity in procedures as the allergen provocation tests, in particular such tests targeting the skin. Intradermal skin tests are used for the biological evaluation of recombinant allergens and for validation of genetically engineered hypoallergenic derivatives. Intradermal testing in a dog is performed by administering injections of small amounts of allergen solutions directly into the dog's dermis. This is done with small-gauge (27 gauge) needles and injections of 0.05 to 0.1 mL at each site. The positive reactions are arbitrarily interpreted by the presence of erythema, turgidity, height, and size of the wheal. The advantage of the intradermal test is a high sensitivity. This is of particular importance if the test shall deliver a quantitative measure for allergenicity. Performing said test by Griffin et al. with the iMAT molecules according to the present invention, those iMAT molecules show a 10-, 100- to 1000-times or even higher molar concentration of the allergenic component as compared to the corresponding natural, native allergen applied in the same test to reach a positive reaction in sensitized individuals, as for example cats and dogs.

The term “epitope”, herein also interchangeably referred to as “antigenic determinant”, in the course of the present invention refers to the part of an antigen that is recognized by the immune system, either by B-cells or T-cells. Epitopes are presented on the surface of antigen presenting cells by means of MEW molecules to which they are bound.

The term “subject”, herein also interchangeably referred to as “individual” and/or “organism” and/or “host”, in the course of the present invention preferably refers to animals and/or humans, e.g. ruminants, pigs, more preferably dogs and/or cats, but excluding equines. The term “ruminant”, in the course of the present invention encompasses ruminating mammals including cattle, goats, and sheep. Thus, members of the genus Bos, Capra and/or Ovis, are interchangeably referred to as “bovine”, “caprine” and/or “ovine” species. The term “animal” as used herein includes mammals. The animal may be selected from the group consisting of ruminants or members of the genus Canis or interchangeably referred to as “canine” species (e.g. dogs, wolves, foxes, coyotes, jackals), or members of the genus Felis or interchangeably referred to as “feline” species (e.g. lions, tigers, domestic cats, wild cats, other big cats, and other felines including cheetahs and lynx) or pigs, i.e. members of the genus Sus interchangeably referred to as “porcine” species.

The terms “peptide” and “protein” are used side by side as equivalent in the course of the present invention. A peptide or a protein means for the purposes of the present invention a covalent bond of at least two amino acids via a peptide linkage. The term “amino acid” and the term “amino acid residue” are used as equivalents in the present application, i.e. the meaning of the two terms is identical. The terms amino acid/amino acid residue and peptide/protein are used in the present application in the form of the widest possible definition.

In this connection, the term “recombinant protein” refers to a polypeptide which may be obtained by genetic engineering and expression in eukaryotic or prokaryotic systems. In addition, said term encompasses polypeptides obtained by artificial (e.g. solid-phase) synthesis.

As used herein, the term “different amino acid residue” refers to a known amino acid residue other than cysteine unless otherwise indicated. For example, said amino acid residue may be a naturally occurring amino acid residue, such as serine or isoleucine.

As used herein, the term “linear form” refers to proteins according to the present invention that lack secondary structure. Such proteins are often assumed to exhibit a random-coil conformation in which the only fixed relationship is the joining of adjacent amino acid residues by a peptide bond.

In a preferred embodiment, the (isolated) recombinant protein as herein disclosed and claimed is present in monomeric form and/or linear form.

As used herein, the term “treatment” refers to the administration of the (isolated) recombinant protein, as disclosed and claimed herein, and/or the corresponding vaccines and/or immunogenic compositions and/or pharmaceutical compositions in order to obtain the desired clinical results including prophylactic and/or therapeutic treatment.

As used herein, the term “immunotherapy” refers to a therapeutic and/or prophylactic treatment of a subject, e.g. by prophylactic and/or therapeutic vaccination.

As used herein, the term “vector” in connection with “transmission of one or more infectious disease(s)” refers to an alive organism and is herein interchangeably used with terms “biological vector”, “biological carrier” and/or “disease carrier”, such as blood feeding bugs, flies, midges, ticks and/or mosquitos.

Furthermore, it is possible, and preferred, that the (isolated) recombinant protein, as disclosed and claimed herein, contains in addition at least one tag module. That is, it is possible, and preferred, that one or more different and/or identical tag modules are part of the (isolated) recombinant protein, as disclosed and claimed herein. Tag modules may be short peptides, frequently consisting of up to 20 amino acids or functional groups which are not composed of amino acids, such as for example biotin or digoxigenin. Suitable tag modules include the well-known and preferred His-tag containing a histidine sequence of 4 to 12 or more, preferably directly consecutive histidine residues, preferably 5, 6 or 7 consecutive histidine residues. Other suitable tag modules include HA-tag, FLAG-tag, GST-tag or Strep-tag. Although the tag can be present anywhere in the (isolated) recombinant protein, as disclosed and claimed herein, in a preferred embodiment, the tag module is present at the (quasi) N-terminus and/or at the C-terminus of the (isolated) recombinant protein.

The tag modules are useful for isolating the (isolated) recombinant proteins, as disclosed and claimed herein, and in addition allow detecting the presence of such (isolated) recombinant proteins in vitro or in vivo. Furthermore, the tag module optionally together with one or more adjacent amino acid residues from an adjacent module or a linker spacing apart the different modules can be used in order to induce a specific immunologically detectable signal, (e.g. an antibody) in the target subject that can be used as a surrogate marker for immunity and/or duration of immunity. Immunotherapies with the (isolated) recombinant proteins, as disclosed and claimed herein, elicit an antigen-specific, preferably allergen-specific immune response in the target subjects that is qualitatively indistinguishable from the natural immune response after exposure to naturally existing antigens, preferably allergens. Thus, antibodies binding to the antigen module are not suitable for the purpose of being a surrogate marker for the efficiency of the iMAT induced immune modulatory effect. This obstacle can be eliminated by determining the unique, antigen-specific immunological signal obtained by the C-terminal and/or (quasi) N-terminal tag module—optionally together with the adjacent amino acid residues. Hence, it is possible to provide suitable surrogate markers accordingly.

In a preferred embodiment, the (isolated) recombinant protein, as disclosed and claimed herein, further comprises at least one tag module, preferably at least one His-tag, wherein such at least one tag module preferably is present N-terminally and/or C-terminally of the (isolated) recombinant protein, more preferably N-terminally after one methionine residue.

Moreover, the modules of the (isolated) recombinant protein, as disclosed and claimed herein, namely, the at least one translocation module, the at least one targeting module and the at least one antigen module may optionally be spaced apart by one or more spacer modules located between at least two of such modules.

The spacer modules may be, in particular, peptide sequences or organic molecules. Numerous spacer molecules which can be used for the purposes of the invention are known in the art. In addition, it is also possible to use spacer molecules which will be developed or discovered in future for the purposes of the invention. Suitable spacer modules are, inter alia, peptide spacers, crosslinkers, natural or synthetic polymers such as, for example, nucleic acids, substituted or unsubstituted hydrocarbons, etc.

The coupling can take place both by covalent (preferred) and by non-covalent linkages. The spacer modules have the task inter alia of separating the various modules of the (isolated) recombinant protein, as disclosed and claimed herein, from each other in space so that they do not have adverse effects on each other with regard to their functionality. Modules of the (isolated) recombinant protein for the purposes of the invention can be coupled by one or more spacer modules which can be cleaved by chemical and/or enzymatic reactions, e.g. by proteases. It is thus possible to separate the modules of the (isolated) recombinant protein, as disclosed and claimed herein, which are connected by the spacer modules, from each other as required.

In a preferred embodiment, however, in particular if the antigen module is an amino acid sequence derived from at least one full or partial epitope of at least one antigen being at least one allergen, no any such additional spacer modules, i.e. no additional spacer modules between two or more adjacent modules of such first, second and/or third modules at all are present.

Any desired arrangement of the individual modules of the (isolated) recombinant protein, as disclosed and claimed herein, is in general possible. Each module may be present one or more times in the (isolated) recombinant protein. The minimum requirement is the presence of at least one translocation module, at least one targeting module and at least one antigen module. Additional modules, such as tag modules, spacer modules, etc. may optionally be present but do not need to be present. All modules may be present one or more times in the (isolated) recombinant protein, as disclosed and claimed herein. If modules are present more than once, they may be present in the form of identical copies, or different versions of a module may be present in each case in a single copy or in more than one copy. It is also possible for entirely different modules of the same class of modules, e.g. a His-tag module and a biotin-tag module, to be present in the (isolated) recombinant protein, as disclosed and claimed herein. Both modules undertake functionally the same task (tag module) in the (isolated) recombinant protein, but do not need to have anything in common in terms of their molecular structure.

In a preferred embodiment, it is possible that two or more copies of one of the modules are present in the (isolated) recombinant protein, as disclosed and claimed herein. That is, two or more copies of identical or different antigen modules may be present. Alternatively, the (isolated) recombinant protein may contain two different antigen modules, for modulating the immune response in a subject.

Two or more identical copies of an antigen module in a recombinant protein may for example cause an enhanced immune response to such relevant antigen. Two or more different antigen modules may for example be combined in one (isolated) recombinant protein in order to modulate simultaneously the immune response towards two or more different antigens. Two or more different translocation modules can be used in the (isolated) recombinant protein, as disclosed and claimed herein. For example, a Tat sequence and a VP22 sequence can serve to make translocation more efficient since the translocation of the (isolated) recombinant protein then takes place efficiently in a broader spectrum of different cell types or tissue types. It is also possible for example to use two or more tag modules in one (isolated) recombinant protein, e.g. a His-tag and a FLAG-tag, in which case for example the His-tag is used to isolate the recombinant protein and for example the FLAG-tag serves to detect the (isolated) recombinant protein. It is possible to use two or more different targeting modules in one (isolated) recombinant protein, e.g. a sequence from the invariant chain of the MHC II molecule and as a further targeting module a mannose 6-phosphate group. For example, the invariant chain acts as targeting module into the MIICs, and the mannose 6-phosphate group mediates targeting into the lysosome, thus it being possible to increase the efficiency of antigen presentation or the number of different epitopes of the antigen presented by the antigen-presenting cells overall. In addition, the iMAT molecule of the present invention may encompass two or more different invariant chains stemming from identical or different species, thus, allowing using the proteins according to the present invention in different species.

The position of the individual modules within the (isolated) recombinant proteins, as disclosed and claimed herein, can also be varied as desired, as long as at least one translocation module, at least one targeting module and at least one antigen module are present. It is also possible for all or some of the modules of the (isolated) recombinant protein for example to be present not in the form of a linear sequential arrangement of modules, but as circular or as branched module structure or else in the form of dendrimers, or as a combination of linear and/or branched and/or circular and/or dendrimeric molecule portions. There are commercial suppliers of expression vectors which supply specific vectors which make it possible to prepare circular fusion proteins by these mechanisms, such as, for example, the IMPACT″-TWIN system from New England Biolabs, Beverly, Mass., USA. Branched modules might be prepared for example by synthesizing peptides in which, starting from poly L-lysine, a new lysine residue is attached to both free amino groups of each of the subsequent lysine residues. In this way it is possible to create a peptide structure with virtually any extent of branching. It is then possible to synthesize, for example, translocation modules and/or targeting modules subsequently onto the branched peptide basic structure. Further modules can also be coupled onto a linear, circular or branched peptide basic structure by protein ligation. It is also possible to introduce for example biotin groups into the peptide basic structure during the peptide synthesis, and modules can then be attached to these biotin groups via, for example, streptavidin, the Strep tag system or via the PINPOINT™ system (respectively IBA GmbH, Gottingen, Germany and Promega Biosciences Inc., San Louis Obispo, Calif., USA). Modules attached in this way are then coupled via non-covalent linkages to the peptide's basic structure.

The antigen module of iMAT molecules according to the present invention can be selected by a bioinformatics approach as described exemplarily and in detail in Examples 5 and 6 herein. By this means iMAT molecules can be rendered useful specifically as vaccines, e.g. for therapy and/or prevention of allergic diseases on the bases of the participation of allergen specific IgE mediated hypersensitivity reactions in different target organs as skin, respiratory—as well as gastrointestinal system, like atopic dermatitis (AD), food allergies and/or allergic asthma in subjects, preferably animals, more preferably dogs and/or cats, but excluding equines.

In a preferred embodiment, the (isolated) recombinant protein relates to, comprises, preferably consists of one or more of the amino acid sequences according to SEQ ID NOs:24 to 83.

The (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in subjects, such animals, more preferably dogs and/or cats, but excluding equines, suffering from allergic diseases on the bases of the participation of allergen specific IgE mediated hypersensitivity reactions in different target organs, e.g. skin, respiratory—as well as gastrointestinal system.

In veterinary medicine allergies are of major importance in particular in the field of companion animals.

Dogs and cats suffer from such diseases, as e.g. canine atopic dermatitis or feline atopic dermatitis or feline asthma.

Canine or feline atopic dermatitis (AD) has been defined as a genetically predisposed inflammatory and pruritic allergic skin disease with characteristic clinical features. It is most commonly associated with IgE antibodies to environmental allergens. The atopic phenotype can be seen in animals with IgE-mediated skin disease, food allergy, or a condition called “atopic-like dermatitis” (ALD). ALD is defined as a pruritic skin disease in dogs with characteristic features of AD but negative tests for IgE antibodies. Feline atopic dermatitis has many similarities to canine atopic dermatitis. Common clinical signs in canine atopic dermatitis include a history of seasonal or non-seasonal pruritus, otitis externa, recurrent and chronic inflammatory dermatitis especially in the axillary, inguinal, and flexor skin surfaces, recurrent bacterial infections, face rubbing and/or foot licking and chewing.

The etiology and pathogenesis of AD is complex and involves a genetic predisposition, impairment of the normal barrier function of the skin, and immunologic aberrations. Animals with AD are thought to be genetically predisposed to become sensitized to allergens in the environment. Allergens are proteins that, when inhaled or absorbed through the skin, respiratory tract, or GI tract, evoke allergen-specific IgE production. These allergen-specific IgE molecules affix themselves to tissue mast cells or basophils via the FCC receptors on such cells. When these primed cells come in contact with the specific allergen again, mast cell degranulation results in the release of proteolytic enzymes, histamine, bradykinins, and other vasoactive amines, leading to inflammation (erythema, edema, and pruritus). The skin is the primary target organ in dogs and cats, but rhinitis and asthma can also occur in ˜15% of affected animals.

Mites are known as major causes of allergic diseases such as atopic dermatitis and asthma in e.g. dogs and cats. Conventionally, desensitization therapy that uses causative substances of allergies as therapeutic agents for allergic diseases is regarded as the most important basic remedy. In particular, the desensitization therapy is broadly conducted for diseases such as pollinosis, house dust allergies, and fungal allergies, which are induced by antigens such as inhalant allergens that are difficult to avoid. However, the desensitization therapy involves the risk of adverse events in particular anaphylaxis due to the action of sensitizing antigens, so that administration of safe therapeutic antigens like iMAT molecules is required.

Regarding mite allergic diseases, several species have been described to be of relevance Dermatophagoides pteronyssinus, Dermatophagoides farinae, Euroglyphus maynei, Dermatophagoides siboney, Dermatophagoides microceras, Lepidoglyphus destructor, Blomia tropicalis, Tyrophagus putrescentiae, Glycophagus domesticus, Acarus siro. However, two types of mites, Dermatophagoides pteronyssinus and Dermatophagoides farinae, have been reported as main allergen sources in house dust (Thomas, W R. et al., Chang Gung Med J 2004; 27:563-569). Major mite allergens have been fractionated from these mites.

The group 1 and 2 allergens of Dermatophagoides sp. induce high titers of IgE and Th2 cytokines in 80% of allergic patients. The allergens Der p 3, 5, 6, 7 and 8 induce IgE in about 50% of subjects usually at lower titers. The 92/98 kDa paramyosin (group 11) allergens binds IgE in 80% of allergic subjects and the 98 and 60 kDa chitinase enzymes (Der f 15 and 18) bind IgE from about 70% and 54% of allergic subjects and are important allergens for allergic dogs (McCall C et al., Vet Immunol Immunopath 2001; 78: 231-247).

In general, a variety of environmental allergens as pollens of grasses, trees, weeds, house dust, dust and storage mites and mold and/or mold spores, but also epidermal and insect antigens have been described to contribute to the sensitization of dogs in canine atopic dermatitis (Hill et al. Vet Immunol Immunopathol, 2001; 81(3-4):169-186).

As described above—the atopic phenotype may also be induced by food allergies, a hypersensitivity with a number of clinical manifestations. Besides gastrointestinal alterations (e.g. gastroenteritis, diarrhea or vomiting), food hypersensitivity often manifests in animals as a pruritic dermatitis and/or dermatosis of the face and neck, miliary dermatitis, generalized scaling or symmetrical alopecia. Especially in cats all the entities of the eosinophilic granuloma may be a consequence of hypersensitivity to certain food allergens.

The most common food allergens derive from meat, milk, fish, but also soybeans and/or more in general tinned food and dried food. Especially in the latter also involvement of allergies to additives and/or storage mites are reported (Guaguere E et al. EJCAP, 2009, 19 (3), 234-241; Jackson H A, EJCAP, 2009, 19 (3), 230-233).

Currently veterinary therapeutic options are restricted to symptomatic (e.g. corticoid) treatments and/or eliminating the foodstuff(s) responsible. However, care must be taken to not adversely affect the nutritional balance of the diet. More recently diets containing hydrolyzed proteins are available. Proteins are broken down—thus being less allergenic, which is effective and well-tolerated. However, these diets tend to be costly and little palatable, which can be a mayor limitation for compliance of the animals.

Allergen specific immunotherapy to treat food allergic animals, preferably dogs and/or cats has not yet been applied.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful as a method for specifically addressing the therapy and/or prophylaxis in cats suffering from allergic airway inflammation and/or obstruction (allergic asthma).

Cats spontaneously develop eosinophilic airway inflammation and airway hyper-reactivity that is very similar to human allergic asthma, i.e. feline allergic asthma is a chronic inflammatory disorder of the lower airways that may manifest with acute, life-threatening clinical signs.

Typical treatment involves palliative treatment only (e.g. bronchodilators and/or corticosteroids), but currently no causative treatment is available. Some pilot studies of the university group around Carol Reinero have addressed allergen specific immunotherapy in an animal model of induced Bermuda grass allergic asthma in cats.

Feline allergic asthma is a complex disease, but clearly exposure to airborne allergens plays a pivotal role in the etiology. Clinical remission can be achieved by eliminating the exposure to the aeroallergens. Though, the major antigens involved in triggering feline allergic asthma have not been clearly identified so far. Numerous potential agents are present in the cat's habitual environment e.g. pollen, molds, dust from cat litter, perfumes, room fresheners, carpet deodorizers, hairspray, aerosol cleaners or cigarette smoke. When screened using serum or intradermal skin tests, naturally allergic cats kept in-house had IgE reactivity to many of the same allergens implicated in human allergic asthma, i.e. mainly to house dust and storage mites and/or pollen (Prost C, Rev Fr Allergol Immunol Clin, 2008, 48 (5), 409-413).

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in cats and/or dogs suffering from AD caused by flea bites (FAD).

FAD is one of the most severe skin allergies caused by flea infestations in dogs and cats. FAD can have manifestations of both immediate and delayed-type hypersensitivity. Typically, an immediate hypersensitive response in an animal susceptible to FAD includes wheal formation at the site of a fleabite. Such wheals can develop into a papule with a crust, representative of delayed-type hypersensitivity. Hypersensitive reactions to fleabites can occur in genetically pre-disposed animals as well as in animals sensitized by previous exposure to fleabites. Furthermore, flea bites can cause scratch-related secondary infections as a consequence of the inflammatory irritation of host's erythema, papules, crusts, and alopecia. Previous work found that pets rarely became desensitized to bites of flea once they have been made allergic to them. So besides the elimination of the flea, the alleviation of the animal's distress becomes the challenging problem. Current therapies for this disease include desensitization therapy or using some types of pharmacological intervention. However, each of these therapeutic approaches has some disadvantages. For example, anti-histamine medications could increase drowsiness, dry mouth, difficulty in urination, and constipation; whereas, classical desensitization therapy may cause life-threatening anaphylactic shock. Other disadvantages of these therapies are the high possibility of recrudescence and requirement for long-term treatments. Therefore, novel, effective therapeutic approaches are needed and should be developed in order to overcome unwanted adverse reactions. Effective treatment of FAD has been difficult if not impossible to achieve. FAD afflicts about 15% of cats and dogs in flea endemic areas and the frequency is increasing each year. In a geographical area, effective flea control requires treatment of all animals. One treatment investigators have proposed includes desensitization of animals using flea allergens. However, reliable, defined preparations of flea allergens are needed for such treatments. Whole flea antigen preparations have been used to diagnose and desensitize animals with FAD. Available commercial whole flea extracts, however, comprise only as a minor part saliva proteins and thus are unpredictable in their specific allergen content and, therefore, have limited usefulness. Prior art U.S. Pat. No. 7,629,446 as well as McDermott M J et al. (Molecular Immunology 2000, 37: 361-375) describe the discovery of the allergen Cte f 1 as major allergen in FAD. In this publication, they describe the cloning of the cDNA and characterization of a flea saliva protein, Cte f 1, a major allergen for flea allergic dogs and cats. Native Cte f 1 has a calculated molecular weight of 18 kDa and p1 of 9.3. Mass spectrometry analysis indicates that the native molecule has no post-translational modifications and that all of the 16 cysteines are involved in intramolecular disulfide bonds. However, in the same publication the authors show several isoforms of the recombinant protein. The 16 cysteines in the secreted protein lead to the occurrence of these isoforms which renders purification and thus manufacturing of such a product difficult or even impossible under GMP conditions.

In research dogs experimentally sensitized to flea bite, Cte f 1 is a major allergen. Using E. coli produced rCte f 1 as the antigen in intradermal skin test and in solid phase ELISA, IgE can be detected in 100% of these experimentally sensitized FAD dogs. In addition, competition ELISA performed using sera from 14 sensitized dogs demonstrated that rCte f 1 produced in three different expression systems (E. coli, P. pastoris and baculovirus infected insect cells) could inhibit approximately 95% of the binding of antigen specific IgE to native Cte f1.

The therapeutic potential of immunotherapeutic approaches comprising the Cte f 1 have been demonstrated by J. Jin et al. (Jin J. et al. Vaccine 28 (2010) 1997-2004). They reported that the simultaneous co-immunization with a DNA vaccine and its cognate coded protein antigen (Cte f 1) exhibit the potential to protect animals from FAD in a murine model. Furthermore, in their study they clinically tested this protocol to treat established FAD in cats following flea infestations. They presented data showing therapeutic improvement of dermatitis in these FAD cats following two co-immunizations.

iMAT molecules comprising the modified Cte f 1 sequence substituting the cysteines with other amino acid residues can be included into the iMAT molecule as allergen module together with either the cat or the dog invariant chain in order to achieve an optimized species specific immune-modulatory effect. Surprisingly these molecules (i) allow efficient recombinant protein production in suitable expression systems, (ii) have a substantially reduced safety risk since effector cells as mast cells are activated at much higher concentrations as compared to the unmodified Cte f 1 and (iii) induce a sustained immunological effect and a long lasting clinical improvement after only three injections.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, suffering from infectious diseases caused by bacteria.

The Gram-negative bacterium Campylobacter is the most common bacterial cause of gastroenteritis in domesticated animals, e.g. dogs, cats, pigs, ruminants. Clinical signs are mostly more severe in young mammals. Besides enteritis also abortions and infertility in various species has been reported. The infection is primarily through ingestion—on entry the bacterium needs to overcome the host defense with the expression of a variety of colonization and virulence determinants. A number of those are antigenic surface or outer membrane proteins, their interaction with e.g. epithelial cells of the gastrointestinal tract is essential for colonization, i.e. infection of the host.

In order to solve this medical problem, the at least one antigen module in a campylobacteriosis dedicated (isolated) recombinant protein, as disclosed and claimed herein, may be selected from antigens derived from Campylobacter spp. e.g. flagellin, surface-exposed proteins (CadF and PEB1), or other surface proteins. Improved MAT molecules may be useful specifically as vaccines, e.g. for therapy and/or prevention of campylobacteriosis. The treatment according to the present invention can involve the administration of the iMAT molecule to the offspring and/or can also comprise a treatment of the pregnant mother.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in animals more preferably ruminants, pigs, dogs and/or cats, but excluding equines, suffering from infectious diseases caused by viruses.

For example, West Nile virus (WNV) is a mosquito-transmitted positive-stranded RNA virus grouped within the Japanese encephalitis virus serocomplex of the genus Flavivirus in the family Flaviviridae. The WNV is the causative agent of the disease syndrome also named West Nile Fever. Birds are the natural reservoir hosts, and WNV is maintained in nature in a mosquito-bird-mosquito transmission cycle. However, man, horses, dogs, cats, but also ruminants have been described to be susceptible. Though most WNV infections remain clinically latent—WNV being a potentially neuroinvasive virus, it may cause meningitis or encephalitis. In animals WNV remains frequently unrecognized, but animals might be euthanatized due to severe neurologic signs caused by WNV—including paresis, ataxia, recumbency, and muscle fasciculation, whereas others exhibit mild to severe polioencephalomyelitis.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the prevention of transmission of infectious diseases in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, by vectors, e.g. blood feeding bugs, flies, midges, ticks and/or mosquitos.

The pathogens are delivered into the skin of the mammalian host along with arthropod saliva, which contains a wide variety of bioactive molecules. These saliva components are capable of altering hemostasis and immune responses and may contribute to the ability of the pathogen to induce an infection. The presence of infectious microorganisms in the salivary glands of blood-feeding arthropods itself alters saliva composition, such as changes in the concentration of e.g. apyrase or anti-thrombinase in infected mosquitoes. Vector-associated or saliva components can e.g. alter vaso-activity and/or modulate the immune response of a host and be of crucial importance for transmission of infectious diseases. Vaccination of the host against arthropod saliva components can interfere with viral transmission, as shown for sandfly salivary proteins and transmission of leishmania spp. These vaccines have however not passed preclinical research up to date (WHO PD-VAC 2014—Status of Vaccine Research and Development of Vaccines for Leishmaniasis).

Arthropod saliva antigens are well suited to be employed in the antigen module of iMAT molecules according to the present invention and may be useful specifically as vaccines to activate the host immune system to prevent the transmission of infectious pathogens by vectors e.g. viruses, fungi and/or parasites and/or their pre-patent stages in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, suffering from infectious diseases caused by fungi.

Dermatophytosis or ringworm is a fungal infection of the hair and of the superficial keratinized cell layers of the skin occurring in animals and man. Several species of genus Microsporum or genus Trichophyton belonging to the groups of zoophilic or geophilic dermatophytes can cause clinical infections in mammals. A variety of surface antigens of the fungi and/or their spores are well suited to be employed in the antigen module of iMAT molecules according to the present invention and may be useful specifically as vaccines, e.g. for therapy and/or prevention of dermatophytosis in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in animals more preferably ruminants, pigs, dogs and/or cats, but excluding equines, suffering from infectious diseases caused by parasites.

Parasites infecting mammals are ubiquitous and clinically important across the world. The major parasitic threats to ruminants, pigs, dogs and/or cats are e.g. Cooperia, Haemonchus, Ostertagia, Trichostrongylus, Dictyocaulus, Metastrongylus. Increasing levels of anthelmintic resistance is reported worldwide in parasites. For protozoa, e.g. Cryptosporidium few drugs consistently inhibit parasite infestation and/or reproduction in the host. Mainly neonatal or young mammals are affected and outcome relies on innate and adaptive immune responses.

Antigens deriving from adult parasites as well as prepatent stages are another example to be employed in the antigen module of iMAT molecules according to the present invention and may be useful specifically as vaccines, e.g. for therapy and/or prevention of parasite infection in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines.

The treatment according to the present invention can involve the administration of the iMAT molecule to the offspring and/or can also comprise a treatment of the pregnant mother.

In particular, in case of modulating the immune response in canine, feline, bovine, ovine, caprine or porcine species the at least one targeting module preferably is the respective invariant chain.

In a preferred embodiment the at least one targeting module is the canine invariant chain according to SEQ ID NO: 2 or 4. In another preferred embodiment the at least one targeting module is the feline invariant chain according to SEQ ID NO: 3 or 5.

In an advantageous embodiment, the (isolated) recombinant protein, as disclosed and claimed herein, is present in a monomeric form since, for instance, recombinant allergens tend to aggregate formation, particularly, if produced via inclusion bodies. By substituting at least one, preferably all cysteine residues in the entire sequence of the (isolated) recombinant protein, preferably by substituting for serine, leucine, isoleucine, arginine, methionine and/or aspartic acid, it is possible to prevent intermolecular disulfide bond formation, thus, avoiding any aggregation, in particular, any non-native formation of inter- and/or intramolecular bonds. That is, the (isolated) recombinant protein being entire devoid of cysteine residues does not aggregate. Consequently, the protein is easily to express and demonstrates improved targeting and MHC presentation.

Furthermore, such cysteine-free variants of, for instance, allergens, in which the cysteine residues in the amino acid sequence of wild-type allergens have been mutated solely or in combinations, show a reduced IgE reactivity compared to the corresponding wild-type allergens and at the same time have substantially retained reactivity towards T-lymphocytes and are thus hypoallergenic.

The invention accordingly relates to such hypoallergenic variants of allergens eliciting for example allergies to flea bites; to certain food components and/or atopic dermatitis and/or allergic airway inflammation and/or obstruction in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, wherein in the variants the cysteine residues of wild-type allergens have been mutated solely or in combination.

Furthermore, the presence of a tag module for separating proteins in a sample, comprising the iMAT molecules according to the present invention, e.g. using zinc- or cobalt-charged solid support further improve the possibility to produce fusion proteins without aggregates during the purification process. Typically, the tag module includes a polyhistidine tag of five to six consecutive histidine residues.

The (isolated) recombinant proteins, as disclosed and claimed herein, are useful in a pharmaceutical composition. For example, the (isolated) recombinant proteins are for use in a vaccine. Hence, the present invention provides vaccine compositions containing one or more (isolated) recombinant proteins, as disclosed and claimed herein. Such vaccine composition can be used therapeutically and/or prophylactically in animals, more preferably dogs and/or cats, but excluding equines, suffering from allergic diseases on the basis of participation of allergen specific IgE mediated hypersensitivity reactions in different target organs such as skins, respiratory and gastrointestinal systems; or such vaccine composition can be used therapeutically and/or prophylactically in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, suffering from infectious diseases induced by pathogens, e.g. viruses, fungi and/or parasites and/or their prepatent stages. Additionally, the method is not only directed against such pathogens, but also capable to activate the host immune system to prevent the transmission of a disease by vectors, e.g. blood feeding bugs, flies, midges, ticks and/or mosquitos.

Thus, in a preferred embodiment of the present invention a vaccine for subjects, such as animals, more preferably dogs and/or cats, but excluding equines, is provided in order to treat and/or prevent atopic dermatitis and/or allergic asthma caused by a response of e.g. exposure to Dermatophagoides mites.

In a further embodiment of the present invention a vaccine for subjects, such as animals, more preferably cats, but excluding equines, is provided in order to treat and/or prevent allergic asthma caused by a response to e.g. mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces).

In a further embodiment of the present invention a vaccine for subjects, such as animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, is provided in order to treat and/or prevent infectious diseases involving e.g. the genera Campylobacter, Dirofilaria, Ehrlichia, Leishmania, Trypanosoma, Borrelia, Orthobunyavirus, Orbivirus, Flavivirus, Rotavirus, Coronavirus, Trichophyton, Microsporum; other helminths like Cooperia, Haemonchus, Ostertagia, Trichostrongylus, Dictyocaulus, Metastrongylus; and/or protozoa with gastrointestinal infestation like Eimeria, Isospora, Cryptosporidium, Giardia—in case of parasites also antigens derived from the prepatent stages might be employed. Additionally, the vaccine can be provided to activate the host immune system to prevent transmission of diseases by vectors, e.g. belonging to the families Culicidae, Ceratopogonidae, Phlebotominae Ixodidae and/or Cimicidae and/or other blood feeding insects.

The pharmaceutical composition, e.g. in form of a vaccine, of the (isolated) recombinant proteins is preferably designed for sublingual administration, subcutaneous and/or intradermal injection, injection into a lymph node and/or for administration via the mucous membranes, in particular, via the mucous membranes of the gastrointestinal tract or of the respiratory system.

In a preferred embodiment of the present invention, the pharmaceutical compositions are parenterally administered.

The iMAT molecules according to the present invention can be used as a pharmaceutical or as a vaccine to modify, for instance, allergic disorders. For example, atopic dermatitis and/or allergic asthma can be treated by such iMAT molecules.

Low amounts (1 to 1000 μg referring to the weight of solely the one or more antigen modules) of recombinant iMAT molecules comprising allergens of atopic dermatitis and/or allergic asthma eliciting from mites of the genus Dermatophagoides e.g. injected 1 to 5 times subcutaneously, intradermally or directly into the lymph node, induce a strong and long lasting immune response in cat and/or dog leading to prevention of the disease and/or an amelioration of clinical symptoms.

In one preferred embodiment, the iMAT molecules of the present invention are administered in combination with at least one adjuvant. The adjuvant includes, but is not limited to, one or more of the following: alum, BCG, aluminium hydroxide, aluminium phosphate, calcium phosphate, lipid emulsions, lipid or polymeric nano- or microspheres, micelles, liposomes, saponin, lipid A, or muramyl dipeptide, bacterial products, chemokines, cytokines and hormones, chitosan, starch, alginate, cellulose derivatives (e.g., ethyl cellulose, hydroxypropylmethyl cellulose), nucleic acids, or a nucleic acid construct. One or more of these components may be added to enhance or modify the immune response. Alternatively, the iMAT molecule may be administered without an adjuvant or in an aqueous form.

The iMAT molecules may be administered in a dose of about 1 μg to 1000 μg (this and the subsequent doses referring to the weight of solely the one or more antigen modules) and more preferably in a dose from about 10 μg to about 100 μg and even more preferably in a dose from about 20 μg to about 50 although the optimal dose may vary depending on the antigen, preferably allergen, being injected, the weight of the subject, the immune system of the subject, and alike. Effective treatment in many cases may be accomplished with one administration. In some embodiments, treatment includes 1 to 15 administrations. In preferred embodiments, treatment includes 1 to 5 administrations and more preferably 1 to 3 administrations. For initial treatment administrations may be periodically, e.g. over a course of days, once or twice per month or year, or several times a year. For maintenance of immune response, administrations may be done in intervals of several months to several years.

In a preferred embodiment of the present invention, the (isolated) recombinant proteins, as disclosed and claimed herein, are designed for lymphatic intranodal administration. In the course of direct injection into a lymph node, the respective lymph node may be visualized during the injection procedure e.g. by ultrasound, in order to monitor the location of the needle and changes in the lymph node, such as swelling. Injection into the mandibular, axillary, inguinal and/or popliteus lymph nodes is preferred due to ease of ultrasound guided location and injection.

It is known in the art that several of the identified proteins from mites in feces and from whole mite bodies induce IgE reactivity and pathological dermal and respiratory reactions in dogs and/or cats [Allergome (www.allergome.org)]. Thus, it is expected that a treatment can only be successful, if most of the relevant allergens are included in a medicine for specific immunotherapy. However, surprisingly only 1, 2, 3 or 4 of such iMAT molecules according to the present invention each comprising different antigen modules e.g. of mites or a mosaic-like construct of epitopes are sufficient to induce an immunomodulation and/or clinical improvement of the diseased subjects if such iMAT molecules are injected 1 to 5 times subcutaneously, intradermally and/or directly into the lymph node.

In a preferred embodiment, a single iMAT molecule is employed and is sufficient for the induction of a therapeutic effect and/or prevention of development of allergen specific IgE mediated hypersensitivity reactions in different target organs as skin, respiratory and/or the gastrointestinal system e.g. in animals, more preferably dogs and/or cats, but excluding equines. Prevention and/or therapy of infectious diseases and/or prevention of transmission of infectious diseases by vectors can be achieved in animals, preferably ruminants, pigs, dogs and/or cats, but excluding equines.

In another preferred embodiment, a combination of 2, 3 or 4 iMAT molecules is employed by means of simultaneous, sequential and/or a chronologically staggered co-administrations.

In a preferred embodiment, a single iMAT molecule is employed and is sufficient for the induction of a therapeutic effect and/or prevention and/or prevention of transmission of infectious diseases in animals, more preferably ruminants, pigs, dogs and/or cats, but excluding equines, e.g. induced by viruses, fungi and/or parasites and/or their prepatent stages and/or the transmission of such infectious diseases by e.g. blood feeding bugs, flies, midges, ticks and/or mosquitos.

In another preferred embodiment, a combination of 2, 3 or 4 iMAT molecules is employed by means of simultaneous, sequential and/or a chronologically staggered co-administrations.

Depending on the thermodynamic evaluation of the (isolated) recombinant protein, as herein disclosed and claimed, stability is influenced by the cysteine mutation, namely the substituting different amino acid residue(s). For example, the substitution may be a Cys to Ser substitution. However, the stability may be higher using a different amino acid residue than the Ser amino acid to achieve the desired stability and solubility. That is, while a first choice may be substitution of Cys with Ser, in case of instability other amino acid residues than Ser should replace Cys.

In order to select stabilizing amino acid residues as replacements for cysteine residues in targeted sequences a three step approach is chosen:

-   -   1. Modeling the tertiary structure of the targeted protein         including terminal Hexa-Histidine tags, iMAT sequence and the         primary amino acid sequence of the protein of interest. Modeling         can be conducted with the native sequence and with cysteine         substitutions.     -   2. Iterative determination of protein stabilities based on         single point substitutions, such as substitution of a cysteine         residue with a different amino acid residue, e.g. Ser and/or         Ile, and scoring to determine stabilizing replacements by         analyzing all available three dimensional structures.     -   3. Re-Modeling of the stabilized structure and validation of the         stability by repeating step 1 and 2.

Three-dimensional protein structures are crucial for understanding protein function on a molecular level and are of great interest for the rational design of many different types of biological experiments, such as site-directed mutagenesis. However, the number of structurally characterized proteins is small compared to the number of known protein sequences. It is possible to identify a homologous protein with a known structure (template) for a given protein sequence (target). In these cases, homology modeling has proven to be the method of choice to generate a reliable 3D model of a protein from its primary amino acid sequence. Building a homology model comprises four main steps: (1) identification of structural template(s), (2) alignment of target sequence and template structure(s), (3) model building and (4) model quality evaluation. These steps can be repeated until a satisfying modeling result is achieved. In cases where no accurate homologue model can be determined, computational approaches to determine a protein structure from the primary structure (amino acid sequences) are used. “De novo” or “ab initio” methods are based on physical principles and try to imitate the folding process. Such methods have to sample a large number of conformations and require very accurate energy functions to identify structures in the global minima of free energy. Many methods use a combination of these described principles.

The availability of computational tools yielding reasonably accurate estimations of the impact of amino acid substitutions on the stability of proteins is of crucial importance in a wide range of applications. In particular, such tools have the potential of stimulating and supporting protein engineering and design projects dedicated to the creation of modified proteins.

Protein stability can be regarded in terms of the thermodynamic stability of a protein that unfolds and refolds rapidly, reversibly. In these cases, the stability of the protein is the difference in Gibbs free energy between the folded and the unfolded states. The only factors affecting stability are the relative free energies of the folded and the unfolded states. The larger and more positive the folding free energy difference is, the more stable the protein is to denaturation. The folding free energy difference is typically small, of the order of 5-15 kcal/mol for a globular protein. However, on the other hand, protein stability can be regarded as a protein property to withstand harsh temperature or solvent conditions. This is related to the thermodynamic stability but also to reversibility or irreversibly of folding/unfolding (kinetic stability).

To predict the thermodynamic stability changes caused by single site substitutions in proteins, several different approaches can be applied to study the impacts of such substitutions on protein structure and function [Pires D E et al., Bioinformatics 2014, 30(3):335-342]. Such approaches can be broadly classified into those that seek to understand the effects of substitutions from the amino acid sequence of a protein alone, and those that exploit the extensive structural information. Structure-based approaches typically attempt to predict either the direction of change in protein stability on substitutions or the actual free energy value (ΔΔG).

The results for each specific protein and its corresponding models are statistically analyzed in terms of the number of appearances of specific substitutions using a scoring system, that grades the replacement based on occurrences in used models and the protein stability free energy change (ΔΔG) thereby determining most destabilizing residues (if any) within the input structure and possible replacements. The score is calculated by determination of the lowest ΔΔG (ΔΔG<0) at each position of interest in each model and assigning corresponding linear values and cumulative ΔΔG's values for each potential replacement position and results are than evaluated to determine consistency among models. Since calculated protein models possess different qualities (the probability of predicting the correct three-dimensional structure) a weighting factor can be implemented to prioritize results from more accurate models. A significant (based on the ΔΔG) destabilizing residue (if any) is substituted; new models are generated and re-analyzed iteratively until a steady state is reached. Additionally, generated models are evaluated by analyzing the xyz coordinates via principal component analysis to determine potential structural misfoldings due to replacement of amino acids at specific positions.

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing a method of identifying amino acid substitutions in a predetermined amino acid sequence allowing the stabilization of such predetermined amino acid sequence comprising the steps of:

-   -   i. modeling of the three-dimensional/tertiary structure of the         targeted predetermined amino acid sequence,     -   ii. iterative determination of protein stabilities based on         single point substitutions, such as substitutions of cysteine         residues with different amino acid residues, preferably serine         and/or isoleucine residues, and a scoring system based on the         protein stability free energy changes (ΔΔG) to determine         stabilizing substitutions by analyzing all available         three-dimensional/tertiary amino acid sequence structures,     -   iii. re-modeling of the substituted three-dimensional/tertiary         amino acid sequence structure and calculation of its stability         by repeating steps (ii) and (iii) until a steady state is         reached;

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing an (isolated) recombinant protein as herein disclosed and claimed, wherein its full or partial amino acid sequence was stabilized by the method of identifying amino acid substitutions in a predetermined amino acid sequence as herein disclosed and claimed (see Example 5 as well as Example 6 herein).

Sequences

The following protein sequences are detailed and disclosed hereby in the present invention (aa or AA being short for amino acids):

SEQ ID NO: 1 relates to a suitable minimal amino acid sequence for one translocation module according to the present invention which is still being functional, i.e. capable of effectively promoting cell entry->TAT sequence;

SEQ ID NOs: 2-5 Invariant Chains (Full Sequences and 110aa):

SEQ ID NO: 2 relates to the full canine invariant chain amino acid sequence; >gi|545496086|Canis_lupus_familiaris|XP_536468.5| PREDICTED: HLA class II histocompatibility antigen gamma chain isoform X1 [Canis lupus familiaris] SEQ ID NO: 3 relates to the full feline invariant chain amino acid sequence; >gi|410949651|Felis_catus|XP_003981534.1| PREDICTED: HLA class II histocompatibility antigen gamma chain isoform X1 [Felis catus] SEQ ID NO: 4 relates to the first 110 aa of the canine invariant chain amino acid sequence; SEQ ID NO: 5 relates to the first 110 aa of the feline invariant chain amino acid sequence; SEQ ID NO: 6 relates to the N-Terminal Marker of 22 aa

SEQ ID NOs: 7-13 Allergens, Full Sequences:

SEQ ID NO: 7 relates to the full Der f 1 allergen amino acid sequence; >Q58A71 Der f 1 allergen preproenzyme Dermatophagoides farinae (American house dust mite) SEQ ID NO: 8 relates to the full Der f 2 allergen amino acid sequence; >Q00855 Mite group 2 allergen Der f 2 (Allergen Der f II) (allergen Der f 2) Dermatophagoides farinae (American house dust mite) SEQ ID NO: 9 relates to the full Der f 23 allergen amino acid sequence; >A0A088SAW7 Der f 23 allergen Dermatophagoides farinae (American house dust mite) SEQ ID NO: 10 relates to the full Der f 18p allergen amino acid sequence; >Q86R84 60 kDa allergen Der f 18p Dermatophagoides farinae (American house dust mite) SEQ ID NO: 11 relates to the full Der f 15 allergen amino acid sequence; >Q9U6R7 98 kDa HDM allergen (Der f 15 allergen) (Group 15 allergen Der f 15) Dermatophagoides farinae (American house dust mite) SEQ ID NO: 12 relates to the full Zen 1 protein allergen amino acid sequence; >I7HDR2 Zen 1 protein Dermatophagoides farinae (American house dust mite) SEQ ID NO: 13 relates to the full Cte f 1 allergen amino acid sequence; >Q94424 Salivary antigen 1 (FS-I) (allergen Cte f 1) Ctenocephalides felis (Cat flea)

SEQ ID NOs: 14-20 Allergens, IMAT Forms (Short):

SEQ ID NO: 14 relates to the iMAT Form (short) of Der f 1 allergen amino acid sequence; SEQ ID NO: 15 relates to the iMAT Form (short) Der f 2 allergen amino acid sequence; SEQ ID NO: 16 relates to the iMAT Form (short) Der f 23 allergen amino acid sequence; SEQ ID NO: 17 relates to the iMAT Form (short) Der f 18p allergen amino acid sequence; SEQ ID NO: 18 relates to the iMAT Form (short) Der f 15 allergen amino acid sequence; SEQ ID NO: 19 relates to the iMAT Form (short) Zen 1 protein allergen amino acid sequence; SEQ ID NO: 20 relates to the iMAT Form (short) Cte f 1 allergen amino acid sequence; SEQ ID NOs: 21-23 Allergens from Hybrids 1, 2, and 3-IMAT Forms (Short): SEQ ID NO: 21 relates to the iMAT Form (short) Hybrid 1 allergen SEQ ID NO: 22 relates to the iMAT Form (short) Hybrid 2 allergen SEQ ID NO: 23 relates to the iMAT Form (short) Hybrid 3 allergen SEQ ID NOs: 24-44 iMATs for Cat (with N-Terminal or C-Terminal Hexa-Histidine or without Hexa-Histidine/Methionine (IMAT_Pure)): SEQ ID NO: 24 relates to a Der f 1 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 25 relates to a Der f 1 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 26 relates to a Der f 1 iMAT molecule (cat) without tag; SEQ ID NO: 27 relates to a Der f 2 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 28 relates to a Der f 2 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 29 relates to a Der f 2 iMAT molecule (cat) without tag; SEQ ID NO: 30 relates to a Der f 23 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 31 relates to a Der f 23 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 32 relates to a Der f 23 iMAT molecule (cat) without tag; SEQ ID NO: 33 relates to a Der f 18p iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 34 relates to a Der f 18p iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 35 relates to a Der f 18p iMAT molecule (cat) without tag; SEQ ID NO: 36 relates to a Der f 15 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 37 relates to a Der f 15 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 38 relates to a Der f 15 iMAT molecule (cat) without tag; SEQ ID NO: 39 relates to a Zen 1 protein iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 40 relates to a Zen 1 protein iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 41 relates to a Zen 1 protein iMAT molecule (cat) without tag; SEQ ID NO: 42 relates to a Cte f 1 protein iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 43 relates to a Cte f 1 protein iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 44 relates to a Cte f 1 protein iMAT molecule (cat) without tag; SEQ ID NOs: 45-65 iMATs for Dog (with N-Terminal or C-Terminal Hexa-Histidine or without Hexa-Histidine/Methionine (IMAT_Pure)): SEQ ID NO: 45 relates to a Der f 1 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 46 relates to a Der f 1 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 47 relates to a Der f 1 iMAT molecule (dog) without tag; SEQ ID NO: 48 relates to a Der f 2 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 49 relates to a Der f 2 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 50 relates to a Der f 2 iMAT molecule (dog) without tag; SEQ ID NO: 51 relates to a Der f 23 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 52 relates to a Der f 23 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 53 relates to a Der f 23 iMAT molecule (dog) without tag; SEQ ID NO: 54 relates to a Der f 18p iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 55 relates to a Der f 18p iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 56 relates to a Der f 18p iMAT molecule (dog) without tag; SEQ ID NO: 57 relates to a Der f 15 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 58 relates to a Der f 15 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 59 relates to a Der f 15 iMAT molecule (dog) without tag; SEQ ID NO: 60 relates to a Zen 1 protein iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 61 relates to a Zen 1 protein iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 62 relates to a Zen 1 protein iMAT molecule (dog) without tag; SEQ ID NO: 63 relates to a Cte f 1 protein iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 64 relates to a Cte f 1 protein iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 65 relates to a Cte f 1 protein iMAT molecule (dog) without tag; SEQ ID NOs: 66-74 Hybrid/Mosaic-Like iMATs for Cat (N-Terminal or C-Terminal Hexa-Histidine or without Hexa-Histidine/Methionine (IMAT_Pure)): SEQ ID NO: 66 relates to a Hybrid 1 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 67 relates to a Hybrid 1 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 68 relates to a Hybrid 1 iMAT molecule (cat) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 5 and SEQ ID NO: 21); SEQ ID NO: 69 relates to a Hybrid 2 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 70 relates to a Hybrid 2 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 71 relates to a Hybrid 2 iMAT molecule (cat) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 5 and SEQ ID NO: 22); SEQ ID NO: 72 relates to a Hybrid 3 iMAT molecule (cat) with N-terminal Hexa-Histidine tag; SEQ ID NO: 73 relates to a Hybrid 3 iMAT molecule (cat) with C-terminal Hexa-Histidine tag; SEQ ID NO: 74 relates to a Hybrid 3 iMAT molecule (cat) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 5 and SEQ ID NO: 23); SEQ ID NOs: 75-83 Hybrid/Mosaic-Like iMATs for Dog (N-Terminal or C-Terminal Hexa-Histidine or without Hexa-Histidine/Methionine (IMAT_Pure)): SEQ ID NO: 75 relates to a Hybrid 1 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 76 relates to a Hybrid 1 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 77 relates to a Hybrid 1 iMAT molecule (dog) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 4 and SEQ ID NO: 21); SEQ ID NO: 78 relates to a Hybrid 2 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 79 relates to a Hybrid 2 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 80 relates to a Hybrid 2 iMAT molecule (dog) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 4 and SEQ ID NO: 22); SEQ ID NO: 81 relates to a Hybrid 3 iMAT molecule (dog) with N-terminal Hexa-Histidine tag; SEQ ID NO: 82 relates to a Hybrid 3 iMAT molecule (dog) with C-terminal Hexa-Histidine tag; SEQ ID NO: 83 relates to a Hybrid 3 iMAT molecule (dog) without tag (consisting of SEQ ID NO: 1, SEQ ID NO: 4 and SEQ ID NO: 23);

SEQ ID NOs: 84-88 Non-redundant Hybrid Allergens:

SEQ ID NO: 84 relates to A1KXC1_DERFA_DFP1 (UNIPROT database); SEQ ID NO: 85 relates to A0A088SAS1_DERFA Der f 28 allergen (UNIPROT database); SEQ ID NO: 86 relates to B7U5T1_DERFA Der f 6 allergen (UNIPROT database); SEQ ID NO: 87 relates to T2B4F3_DERPT LytFM (UNIPROT database); SEQ ID NO: 88 relates to A7XXV2_DERFA Der f 2 allergen (UNIPROT database);

SEQ ID NOs: 89-90 Miscellaneous Sequences:

SEQ ID NO: 89 relates to a Cul o2 iMAT molecule with N-terminal HEXA-HISTIDINE; SEQ ID NO: 90 relates to a Cul o3 iMAT molecule with N-terminal HEXA-HISTIDINE.

SEQ ID NOs: 91-102 Peptide Components of Hybrids:

SEQ ID NO: 91 relates to a peptide part of a hybrid derived from SEQ ID NO: 10, SEQ ID NO: 92 relates to a peptide part of a hybrid derived from SEQ ID NO: 85, SEQ ID NO: 93 relates to a peptide part of a hybrid derived from SEQ ID NO: 88, SEQ ID NO: 94 relates to a peptide part of a hybrid derived from SEQ ID NO: 86, SEQ ID NO: 95 relates to a peptide part of a hybrid derived from SEQ ID NO: 87, SEQ ID NO: 96 relates to a peptide part of a hybrid derived from SEQ ID NO: 11, SEQ ID NO: 97 relates to a peptide part of a hybrid derived from SEQ ID NO: 7, SEQ ID NO: 98 relates to a peptide part of a hybrid derived from SEQ ID NO: 10, SEQ ID NO: 99 relates to a peptide part of a hybrid derived from SEQ ID NO: 12, SEQ ID NO: 100 relates to a peptide part of a hybrid derived from SEQ ID NO: 9, SEQ ID NO: 101 relates to a peptide part of a hybrid derived from SEQ ID NO: 11, SEQ ID NO: 102 relates to a peptide part of a hybrid derived from SEQ ID NO: 8.

Hybrid/Mosaic-Like iMAT Molecules:

In a specific aspect of the present invention the iMAT molecules are further improved if components (amino acid sequences/epitopes) of more than one allergen are included into the antigen module. For this purpose it is possible to apply the basic principle of the described bioinformatics selection approach (Example 5) in a different way. Instead of selecting complete allergens based on the hit count of allergen peptides found in the allergen database, only the most abundant peptides of several of such allergens are used to engineer an iMAT antigen module (see e.g. Example 6). Thus, such an iMAT molecule consists of an antigen module of peptides that stem from several allergens. This allows broadening of the spectrum of a single iMAT molecule with respect to its targeted immunological profile and is thus beneficial for pharmacological drug development.

As a further step in engineering hybrid iMAT molecules the TAT and the targeting domain, and optionally a His-Tag, are added. Finally cysteine residues are replaced by most stabilizing residues as described in examples 5 and 6.

Hybrid I

A protein precursor is chosen from the list of precursor proteins corresponding to top ranking peptides and used as a scaffold protein (SEQ ID NO: 84) for embedding other top ranking peptides from other antigens (SEQ ID NOS: 10, 11, 85, 86, 87, 88). The signal peptide sequence is removed from the scaffold protein. Optionally additional adjacent N- or C-terminal amino acids are inserted within the original sequence of the scaffold protein and replace parts of the original sequence of the scaffold protein as described below.

Components of the following proteins are employed to construct hybrid 1:

SEQ ID NO: 84 (A1KXC1_DERFA DFP1 OS=Dermatophagoides farina) SEQ ID NO: 10 (Q86R84 DERFA 60 kDa allergen Der f 18p OS=Dermatophagoides farinae GN=Der f 18 PE=2 SV=1) SEQ ID NO: 85 (A0A088SAS1_DERFA Der f 28 allergen OS=Dermatophagoides farinae PE=2 SV=1) SEQ ID NO: 88: (A7XXV2_DERFA Der f 2 allergen OS=Dermatophagoides farinae PE=4 SV=1) SEQ ID NO: 86 (B7U5T1_DERFA Der f 6 allergen OS=Dermatophagoides farinae PE=2 SV=1) SEQ ID NO: 87 (T2B4F3_DERPT LytFM OS=Dermatophagoides pteronyssinus GN=lytFM PE=4 SV=1) SEQ ID NO: 11 (Q9U6R7_DERFA 98 kDa HDM allergen OS=Dermatophagoides farinae PE=2 SV=1)

Backbone of Hybrid 1:

SEQ ID NO: 84 (A1KXC1 18-400, without replacement parts below)

[Replacement 1 for: SEQ ID NO: 84 AA 39-52]:

SEQ ID NO: 10 (Q86R84_AA 97-110) i.e. (SEQ ID NO: 91) GNAKAMIAVGGSTM

[Replacement 2 for: SEQ ID NO: 84 AA 261-274]:

SEQ ID NO: 85 (A0A088SAS1_AA 611-624) i.e. (SEQ ID NO: 92) MMKIYQQQQQQHHP

[Replacement 3 for: SEQ ID NO: 84 AA 234-246]:

SEQ ID NO: 88 (A7XXV2 AA_48-61) i.e. (SEQ ID NO: 93) FLVYIHIANNEIKK

[Replacement 4 for: SEQ ID NO: 84 AA 53-65]:

SEQ ID NO: 86  (B7U5T1 AA_166-178) i.e. (SEQ ID NO: 94) IVDGDKVTIYGWG

[Replacement 5 for: SEQ ID NO: 84 AA 276-289]:

SEQ ID 87: (T2B4F3_AA 134-147) i.e. (SEQ ID NO: 95) REENIWSDHIANVA

[Replacement 6 for: SEQ ID NO: 84 AA 203-216]:

SEQ ID NO: 11 (Q9U6R7_AA 469-482) i.e. (SEQ ID NO: 96) TPTTPTPAPTTSTP

After cysteine residues are replaced by most stabilizing residues applying the bioengineering process described in Examples 5 and 6, this results in SEQ ID NO: 21.

The backbone of hybrid 1 is formed by the amino acid sequence SEQ ID NO: 84. The further peptide components of hybrid 1 antigen module SEQ ID NOs: 91-96 are embedded into the backbone sequence derived from SEQ ID NO: 84. These further peptide components of hybrid 1 antigen module SEQ ID NOs: 91-96 can be arranged in any order/in a different order (if compared to the order of replacement described above). Any such re-arranged peptide order based on the above described antigens/allergens is envisaged by the present invention.

Hybrid 2

Complete allergens and/or top ranking peptides are chosen and spliced together to obtain the allergen module for a given IMAT molecule described below.

Components of the following proteins are employed to construct hybrid 2 in the depicted particular order, whereby part 1 is the N-terminus. The further parts are added according to the below order to the C-terminus of the previous part. In case of hybrid 2 these are 5 further parts. There are 6 parts in total.

Part 1: SEQ ID NO 7 (Q58A71 Der f 1 allergen preproenzyme Dermatophagoides farinae (American house dust mite) AA 99-321) i.e.

(SEQ ID NO: 97) TSACRINSVNVPSELDLRSLRTVTPIRMQG GCGSCWAFSGVAATESAYLAYRNTSLDLSE QELVDCASQHGCHGDTIPRGIEYIQQNGVV EERSYPYVAREQQCRRPNSQHYGISNYCQI YPPDVKQIREALTQTHTAIAVIIGIKDLRA FQHYDGRTIIQHDNGYQPNYHAVNIVGYGS TQGVDYWIVRNSWDTTWGDSGYGYFQAGNN LMMIEQYPYVVIM

Part 2: SEQ ID NO 10 (Q86R84 60 kDa allergen Der f 18p Dermatophagoides farinae (American house dust mite) AA 277-304) i.e.

(SEQ ID NO: 98) FTQTDGFLSYNELCVQIQAETNAFTITR

Part 3: SEQ ID NO 12 (I7HDR2 Zen 1 protein Dermatophagoides farinae (American house dust mite) AA 181-220) i.e.

(SEQ ID NO: 99) EPTTPTPEPTTKTPEPTTKTPEPSTPTPEPTTKTPEPTTK

Part 4: SEQ ID NO 9 (A0A088SAW7 Der f 23 allergen Dermatophagoides farinae (American house dust mite) AA 22-91) i.e.

(SEQ ID NO: 100) DIDHDDDPTTMIDVQTTTVQPSDEFECPTR FGYFADPKDPCKFYICSNWEAIHKSCPGNT RWNEKELTCT

Part 5: SEQ ID NO 11 (Q9U6R7 98 kDa HDM allergen (Der f 15 allergen) (Group 15 allergen Der f 15) Dermatophagoides farinae (American house dust mite) AA 437-463) i.e.

(SEQ ID NO: 101) SPTTPTTTPSPTTPTTTPSPTTPTTTP

Part 6: SEQ ID NO 8 (Q00855 Mite group 2 allergen Der f 2 (Allergen Der f II) (allergen Der f 2) Dermatophagoides farinae (American house dust mite) AA 18-146) i.e.

(SEQ ID NO: 102) DQVDVKDCANNEIKKVMVDGCHGSDPCIIH RGKPFTLEALFDANQNTKTAKIEIKASLDG LEIDVPGIDTNACHFMKCPLVKGQQYDIKY TWNVPKIAPKSENVVVTVKLIGDNGVLAC AIATHGKIRD

After cysteine residues are replaced by most stabilizing residues applying the bioengineering process described in Examples 5 and 6, this results in SEQ ID NO: 22.

However, the above peptide components of hybrid 2 antigen module can be arranged in any order/in a different order (if compared to the order of replacement described above). Any such re-arranged peptide order based on the above described antigens/allergens is envisaged by the present invention.

Hybrid 3

Components of the following proteins are employed to construct hybrid 3 in the depicted particular order, whereby part 1 is the N-terminus. The further parts are added according to the below order to the C-terminus of the previous part. In case of hybrid 3 these are 4 further parts. There are 5 parts in total.

Part 1: SEQ ID NO 7 (Q58A71 Der f 1 allergen preproenzyme Dermatophagoides farinae (American house dust mite) AA 99-321) i.e.

(SEQ ID NO: 97) TSACRINSVNVPSELDLRSLRTVTPIRMQG GCGSCWAFSGVAATESAYLAYRNTSLDLSE QELVDCASQHGCHGDTIPRGIEYIQQNGVV EERSYPYVAREQQCRRPNSQHYGISNYCQI YPPDVKQIREALTQTHTAIAVIIGIKDLRA FQHYDGRTIIQHDNGYQPNYHAVNIVGYGS TQGVDYWIVRNSWDTTWGDSGYGYFQAGNN LMMIEQYPYVVIM

Part 2: SEQ ID NO 10 (Q86R84 60 kDa allergen Der f 18p Dermatophagoides farinae (American house dust mite) AA 277-304) i.e. FTQTDGFLSYNELCVQIQAETNAFTITR (SEQ ID NO: 98)

Part 3: SEQ ID NO 11 (Q9U6R7 98 kDa HDM allergen (Der f 15 allergen) (Group 15 allergen Der f 15) Dermatophagoides farinae (American house dust mite) AA 437-463) i.e.

(SEQ ID NO: 101) SPTTPTTTPSPTTPTTTPSPTTPTTTP

Part 4: SEQ ID NO 8 (Q00855 Mite group 2 allergen Der f 2 (Allergen Der f II) (allergen Der f 2) Dermatophagoides farinae (American house dust mite) AA 18-146) i.e.

(SEQ ID NO: 102) DQVDVKDCANNEIKKVMVDGCHGSDPCIIH RGKPFTLEALFDANQNTKTAKIEIKASLD GLEIDVPGIDTNACHFMKCPLVKGQQYDIK YTWNVPKIAPKSENVVVTVKLIGDNGVLA CAIATHGKIRD

After cysteine residues are replaced by most stabilizing residues applying the bioengineering process described in Examples 5 and 6, this results in SEQ ID NO: 23.

However, the above peptide components of hybrid 3 antigen module can be arranged in any order/in a different order (if compared to the order of the parts described above). Any such re-arranged peptide order based on the above described antigens/allergens is envisaged by the present invention.

Further specific aspects of the present invention:

The invention concerns an amino acid sequence/improved MAT (iMAT) molecule, comprising: (i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MI-IC molecules with antigens, preferably processed antigens, and (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope, of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid, for use in a method of prevention and/or therapy of one or more allergies in animals excluding equines and/or for use in a method of prevention and/or therapy of one or more infectious diseases in animals excluding equines and/or for use in a method of prevention of transmission of one or more infectious diseases in animals excluding equines and/or for use in a method of prevention of transmission of one or more infectious diseases in animals excluding equines by vectors.

The invention further concerns a method of prevention and/or therapy of one or more allergies in animals excluding equines and/or a method of prevention and/or therapy of one or more infectious diseases in animals excluding equines and/or a method of prevention of transmission of one or more infectious diseases in animals excluding equines, preferably by vectors, comprising administering a therapeutic effective amount of an amino acid sequence/improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MI-IC molecules with antigens, preferably processed antigens, and (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope, of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

In a specific aspect the at least one antigen module all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. Preferably all cysteine residues in the entire iMAT molecule are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

In a further aspect all of such modules are covalently linked to each other, optionally by additional spacer module(s) between two or more adjacent modules, optionally between all of such first, second and/or third modules.

In a preferred aspect all of such modules are covalently linked to each other, and no additional spacer module(s) between two or more adjacent modules of such first, second and/or third modules are present at all.

In another aspect the at least one second module comprises the invariant chain selected from the canine, feline, bovine, ovine, caprine and/or porcine species' or a partial sequence thereof, provided that such at least one second module is functional as a module allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or loading of MHC molecules with antigens, preferably processed antigens. A preferred canine invariant chain sequence is SEQ ID NO: 2. A preferred feline invariant chain sequence is SEQ ID NO: 3.

In a preferred aspect the at least one second module comprises, preferably consisting of, the amino acid sequence according to SEQ ID NO: 4 (canine) or SEQ ID NO: 5 (feline). SEQ ID NOs: 4 and 5 represent 110 amino acid residues of the invariant chains of SEQ ID NOs: 2 and 3, respectively.

In another preferred aspect the at least one second module comprises, preferably consisting of, the amino acid sequence according to SEQ ID NO: 4 (canine) or SEQ ID NO: 5 (feline) or fragments thereof, provided such fragments maintain their intracellular transport function.

In a further aspect the at least one antigen module comprises at least one full or partial amino acid sequence, preferably an epitope, derived from at least one allergen eliciting an allergy in animals excluding equines, preferably at least one full or partial amino acid sequence, preferably an epitope, of at least one allergen derived from preferably allergies to flea bites, preferably in dogs and/or cats; allergies to certain food components, preferably in dogs and/or cats; atopic dermatitis, preferably in dogs and/or cats; allergic airway inflammation and/or obstruction, preferably in cats.

In a preferred aspect such at least one antigen, preferably at least one allergen, is Der f 15 allergen according to SEQ ID NO: 11 or 18. In a preferred aspect such at least one antigen module comprises, preferably consists of, SEQ ID NO: 18.

In a specific aspect such at least one antigen, preferably at least one allergen, is derived from food and/or mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces) and/or fleas, preferably from pollen from tree, grass, herbaceous, Ambrosia and/or brassicaceae pollen and/or fungi and/or their spores of the genera Aspergillus, Alternaria, Botrytis, Cercospora, Cladosporium, Curvularia, Drechslera, Eurotium, Helminthosporium, Epicoccum, Erysipheloidium, Fusarium, Lichtheimia, Nigrospora, Penicillium, Periconia, Peronospora, Polythrincium, Saccharopolyspora (formerly also Faenia or Micropolyspora), Thermoactinomyces, Stemphylium, torula and/or mites (or their feces) of the genera Acarus, Glycophagus, Tyrophagus, Dermatophagoides, Euroglyphus, Lepidoglyphus, Blomia and/or fleas of the genera Ceratophyllus, Ctenocephalides, Pulex, Archaeopsylla, and more preferably is a Dermatophagoides allergen.

In yet another specific aspect the at least one antigen module comprises at least one full or partial amino acid sequence, preferably an epitope, derived from at least one antigen of a pathogen eliciting one or more infectious diseases in animals excluding equines, preferably at least one full or partial amino acid sequence, preferably an epitope, of at least one antigen of a pathogen eliciting one or more infectious diseases in animals excluding equines selected from the genera Campylobacter, Dirofilaria, Ehrlichia, Leishmania, Trypanosoma, Borrelia, Orthobunyavirus, Orbivirus, Flavivirus, Rotavirus, Coronavirus, Trichophyton, Microsporum; Cooperia, Haemonchus, Ostertagia, Trichostrongylus, Dictyocaulus, Metastrongylus; Eimeria, Isospora, Cryptosporidium, Giardia, wherein preferably the at least one antigen module may also be an antigen of a vector involved in the transmission of one or more infectious diseases in animals excluding equines, preferably an antigen selected from saliva components of vectors selected from blood feeding bugs, flies, midges, ticks and/or mosquitos.

In a preferred aspect the iMAT molecule further comprises at least one tag module, preferably at least one His-tag. Preferably such at least one tag module is present N-terminally. In another preferred specific aspect such at least one tag module is present C-terminally. In another preferred specific aspect such at least one tag module is present N-terminally and C-terminally.

In a specific preferred aspect the iMAT molecule comprises one tag module, preferably one His-tag, N-terminally after one methionine residue.

In another specific preferred aspect there is no tag module present in the iMAT molecules.

In a further aspect the at least one first module comprises, preferably consists of, the amino acid sequence of HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof, provided that such at least one first module is functional as a module for translocation of the iMAT molecule from the extracellular space into the interior of cells, most preferably is amino acid sequence YGRKKRRQRRR (SEQ ID NO: 1).

In another aspect the iMAT molecule is present in monomeric form and/or in linear form.

In a further aspect at least one third module comprises, preferably consists of, any one of SEQ ID NOs: 14 to 23.

In a preferred aspect the iMAT molecule comprises, preferably consists of, one or more of the amino acid sequences according to SEQ ID NOS: 24 to 83.

A specifically preferred iMAT molecule comprises, preferably consists of, SEQ ID NO: 36 (Der f15 iMAT molecule cat) or SEQ ID NO: 57 (Der f15 iMAT molecule dog). Further preferred iMAT molecules (comprising an N-terminal His-tag) are selected from the group consisting of: SEQ ID NOs: 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81. Further preferred iMAT molecules (comprising a C-terminal His-tag) are selected from the group consisting of: SEQ ID NOs: 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58, 61, 64, 67, 70, 73, 76, 79, 82. Further preferred iMAT molecules (without His-tag) are selected from the group consisting of: SEQ ID NOs: 26, 29, 32, 35, 38, 41, 44, 47, 50, 53, 56, 59, 62, 65, 68, 71, 74, 77, 80, 83.

Further preferred iMAT molecules (hybrid/mosaic-like iMATs) are selected from the group consisting of: SEQ ID NOs: 66-83. Further preferred hybrid iMAT molecules are 66, 69, 72, 75, 78, 81 (with N-terminal His-tag). Especially preferred is SEQ ID NO: 66 and/or 75. Further preferred specific hybrid iMAT molecules are 67, 70, 73, 76, 79, 82 (with C-terminal His-tag). Especially preferred is SEQ ID NO: 67 and/or 76. Further preferred specific hybrid iMAT molecules are 68, 71, 74, 77, 80, 83 (without His-tag). Especially preferred is SEQ ID NO: 68 and/or 77.

In a further aspect the animal is selected from ruminants, including cattle, goats, sheep, such as members of the genus Bos, Capra and/or Ovis, members of the genus Canis, such as dogs, wolves, foxes, coyotes, jackals, members of the genus Felis, such as lions, tigers, domestic cats, wild cats, other big cats, and other felines including cheetahs and lynx, and/or members of the genus Sus, such as pigs, wherein preferably the animal is selected from cats and/or dogs.

The invention concerns an amino acid sequence, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of WIC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope, of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. The third module preferably comprises, more preferably consists of any one of SEQ ID NOs: 14 to 23.

The invention concerns an improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of WIC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope, of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. The third module preferably comprises, more preferably consists of any one of SEQ ID NOs: 14 to 23.

In a specific aspect the at least one antigen module all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid, Preferably all cysteine residues in the entire iMAT molecule are substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

In a further aspect all of such modules are covalently linked to each other, optionally by additional spacer module(s) between two or more adjacent modules, optionally between all of such first, second and/or third modules.

In a preferred aspect all of such modules are covalently linked to each other, and no additional spacer module(s) between two or more adjacent modules of such first, second and/or third modules are present at all.

In another preferred aspect the at least one second module comprises, preferably consisting of, the amino acid sequence according to SEQ ID NO: 4 (canine) or SEQ ID NO: 5 (feline) or fragments thereof, provided such fragments maintain their intracellular transport function. SEQ ID NOs: 4 and 5 represent 110 amino acid residues of the invariant chains of SEQ ID NOs: 2 and 3, respectively. In a more preferred aspect the at least one second module comprises, preferably consists of, the amino acid sequence according to SEQ ID NO: 4 (canine) or SEQ ID NO: 5 (feline).

In a further aspect the at least one antigen module comprises at least one full or partial amino acid sequence, preferably an epitope, derived from at least one allergen eliciting an allergy in animals excluding equines, preferably at least one full or partial amino acid sequence, preferably an epitope, of at least one allergen derived from preferably allergies to flea bites, preferably in dogs and/or cats; allergies to certain food components, preferably in dogs and/or cats; atopic dermatitis, preferably in dogs and/or cats; allergic airway inflammation and/or obstruction, preferably in cats.

In a specific aspect such at least one antigen comprises the amino acid sequence according to SEQ ID NO: 11 or 18. In a preferred aspect such at least one antigen, preferably at least one allergen, is Der f 15 allergen according to SEQ ID NO: 11 or 18. In another preferred aspect such at least one antigen module comprises, preferably consists of, SEQ ID NO: 18.

In a further preferred aspect the iMAT molecule comprises, preferably consists of, an (one) amino acid sequence according to SEQ ID NOs: 24 to 83 (one of those alternatives). In a further preferred aspect the iMAT molecule comprises, preferably consists of, any one of SEQ ID NOs: 36-38 (Der f15 iMAT molecule cat), most preferably SEQ ID NO: 36, or the iMAT molecule comprises, preferably consists of, any one of SEQ ID NOs: 57-59 (Der f15 iMAT molecule dog), most preferably SEQ ID NO: 57.

In a preferred aspect the iMAT molecule further comprises at least one tag module, preferably at least one His-tag. Preferably such at least one tag module is present N-terminally. In a specific preferred aspect the iMAT molecule comprises one tag module, preferably one His-tag, N-terminally after one methionine residue.

Preferred iMAT molecules with N-terminal His-tag comprise, preferably consist of, any one of SEQ ID NOs: 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81.

In another specific preferred aspect such at least one tag module is present C-terminally. In another specific preferred aspect such at least one tag module is present N-terminally and C-terminally. Preferred iMAT molecules with C-terminal His-tag comprise, preferably consist of, any one of SEQ ID NOs: 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58, 61, 64, 67, 70, 73, 76, 79, 82.

In another specific preferred aspect there is no tag module present. Preferred iMAT molecules without any tag at all comprise, preferably consist of, any one of SEQ ID NOs: 26, 29, 32, 35, 38, 41, 44, 47, 50, 53, 56, 59, 62, 65, 68, 71, 74, 77, 80, 83.

In a further aspect the at least one first module comprises, preferably consists of, the amino acid sequence of HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof, provided that such at least one first module is functional as a module for translocation of the iMAT molecule from the extracellular space into the interior of cells, most preferably is amino acid sequence YGRKKRRQRRR (SEQ ID NO: 1).

In another aspect the iMAT molecule is present in monomeric form and/or in linear form.

In a further specific aspect the iMAT molecule is a hybrid iMAT molecule (mosaic-like iMAT molecule). Preferably such hybrid iMAT molecule comprises an amino acid sequence according to any one of SEQ ID NOs: 21-23. More specifically such hybrid iMAT molecule comprises, preferably consists of, an amino acid sequence according to any one of SEQ ID NOs: 66-83.

The invention furthermore concerns an amino acid sequence comprising, preferably consisting of, one or more of the amino acid sequences according to SEQ ID NOs: 24 to 83.

The invention further concerns an iMAT molecule comprising, preferably consisting of, one or more of the amino acid sequences according to SEQ ID NOs: 24 to 83.

The invention further concerns an amino acid sequence/iMAT molecule comprising, preferably consisting of, one or more amino acid sequences selected from the group consisting of: SEQ ID NOs: 24 to 83.

A specifically preferred amino acid sequence/iMAT molecule comprises, preferably consists of, SEQ ID NO: 36 (Der f15 iMAT molecule cat) or SEQ ID NO: 57 (Der f15 iMAT molecule dog). Further preferred amino acid sequences/iMAT molecules (comprising an N-terminal His-tag) are selected from the group consisting of: SEQ ID NOs: 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81. Further preferred amino acid sequences/iMAT molecules (comprising a C-terminal His-tag) are selected from the group consisting of: SEQ ID NOs: 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58, 61, 64, 67, 70, 73, 76, 79, 82. Further preferred amino acid sequences/iMAT molecules (without His-tag) are selected from the group consisting of: SEQ ID NOs: 26, 29, 32, 35, 38, 41, 44, 47, 50, 53, 56, 59, 62, 65, 68, 71, 74, 77, 80, 83.

Further preferred amino acid sequences/iMAT molecules (hybrid/mosaic-like iMATs) are selected from the group consisting of: SEQ ID NOs: 66-83. Further preferred hybrid iMAT molecules are 66, 69, 72, 75, 78, 81 (with N-terminal His-tag). Further preferred hybrid iMAT molecules are 67, 70, 73, 76, 79, 82 (with C-terminal His-tag). Further preferred hybrid iMAT molecules are 68, 71, 74, 77, 80, 83 (without His-tag).

The invention concerns an amino acid sequence/improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope sequence, of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 9, 10, 11, 12, 84, 85, 86, 87, and 88 determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

In a preferred aspect the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope sequence, of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 10, 11, 84, 85, 86, 87, and 88 (Hybrid 1).

In a specific aspect the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope sequence, of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 9,10, 11, and 12 (Hybrid 2).

In a specific aspect the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence, preferably an epitope sequence, of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 10, and 11 (Hybrid 3).

Thus, the invention specifically concerns an amino acid sequence/improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence based on a backbone derived from SEQ ID NO: 84 comprising any combination of one or more of the peptides according to SEQ ID NOs: 91-96 (in any order) embedded into said backbone sequence, determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid.

In a preferred aspect the order of peptide sequences within the backbone derived from SEQ ID NO: 84 in the third module is SEQ ID NO: 91, followed by SEQ ID NO: 92, followed by SEQ ID NO: 93, followed by SEQ ID NO: 94, followed by SEQ ID NO: 95, followed by SEQ ID NO: 96 starting from the N-terminus. In a most preferred aspect the third module comprises, preferably consist of, SEQ ID NO: 21.

In a further specific aspect the order of peptide sequences within the backbone derived from SEQ ID NO: 84 in the third module is SEQ ID NO: 93, followed by SEQ ID NO: 91, followed by SEQ ID NO: 92, followed by SEQ ID NO: 94, followed by SEQ ID NO: 96, followed by SEQ ID NO: 95 starting from the N-terminus. Further aspects of the present invention relate to any further combination and order of the peptides according to SEQ ID NOs: 91-96 embedded into the backbone sequence derived from SEQ ID NO: 84.

Thus, the invention further concerns an amino acid sequence/improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of WIC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence derived from any combination of two or more of the peptides according to SEQ ID NOs: 97-102 (in any order), determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. In a preferred aspect the order of peptide sequences within the third module is SEQ ID NO: 97, followed by SEQ ID NO: 98, followed by SEQ ID NO: 99, followed by SEQ ID NO: 100, followed by SEQ ID NO: 101, followed by SEQ ID NO: 102 starting from the N-terminus. In a most preferred aspect the third module comprises, preferably consist of, SEQ ID NO: 22.

In a further specific aspect the order of peptide sequences within the third module is SEQ ID NO: 99, followed by SEQ ID NO: 98, followed by SEQ ID NO: 102, followed by SEQ ID NO: 100, followed by SEQ ID NO: 101, followed by SEQ ID NO: 97 starting from the N-terminus. Further aspects of the present invention relate to any further combination and order of the peptides according to SEQ ID NOs: 97-102.

Thus, the invention additionally concerns an amino acid sequence/improved MAT (iMAT) molecule, comprising:

(i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, preferably said first module comprises, more preferably consists of SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of WIC molecules with antigens, preferably processed antigens, preferably said second module comprises, more preferably consists of, SEQ ID NO: 4 or 5 (iii) at least one third module as antigen module being an amino acid sequence derived from any combination of two or more of the peptides according to SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 101, and SEQ ID NO: 102 (in any order), determining the specificity of an immune response modulated by such iMAT molecule, characterized in that at least in the antigen modules at least one cysteine residue is substituted with a different amino acid residue, preferably serine, leucine, isoleucine, arginine, methionine, and/or aspartic acid. In a preferred aspect the order of peptide sequences within the third module is SEQ ID NO: 97, followed by SEQ ID NO: 98, followed by SEQ ID NO: 101, followed by SEQ ID NO: 102 starting from the N-terminus. In a most preferred aspect the third module comprises, preferably consist of, SEQ ID NO: 23.

In a further specific aspect the order of peptide sequences within the third module is SEQ ID NO: 102, followed by SEQ ID NO: 98, followed by SEQ ID NO: 101, followed by SEQ ID NO: 97 starting from the N-terminus. Further aspects of the present invention relate to any further combination and order of the peptides according to SEQ ID NOs: 97, 98, 101, and 102.

The invention further concerns a vaccine or immunogenic composition or a pharmaceutical composition comprising the amino acid sequence/iMAT molecule according to the present invention.

The invention furthermore concerns a nucleic acid encoding the amino acid/iMAT molecule according to the present invention.

Additionally, the invention concerns a vector comprising at least one nucleic acid according to the present invention.

Furthermore, the invention concerns a primary cell or cell line comprising at least one nucleic acid according to the present invention and/or at least one vector according to the present invention.

The invention additionally concerns a method of identifying improved MAT molecules comprising the steps of:

a) selecting a protein as allergen module in iMAT molecules, and b) constructing an iMAT molecule with said allergens that is thermodynamically stable and can be produced efficiently by protein engineering.

The invention specifically concerns a method of identifying improved MAT molecules comprising the steps of:

a) selecting a protein as allergen module in iMAT molecules that is an allergen and thus has a high potential to cause hypersensitivity in affected subjects and thus can also be the target for tolerance induction, and b) constructing an iMAT molecule with said allergens that is thermodynamically stable and can be produced efficiently by protein engineering and can additionally be analyzed with standard methods to ensure sufficient enough quality (i.e. identity, purity and potency).

In a specific aspect of the method step a) comprises:

selecting (an) allergen(s) based on local homology searches of peptides derived from given proteins to known allergenic proteins,

exporting amino acid sequences of proteins suspected to have allergenic properties from publicly available databases (e.g. UNIPROT),

determining redundancies by analysis of sequences homologies within the exported dataset,

eliminating highly homologue sequence counterparts (remaining sequences serve as the canonical sequence database of probable valid antigens for subsequent analyses),

in silico cleaving proteins into peptides with lengths of 6 to 15 amino acids (with a one amino acid shifting)

performing local-pairwise alignments of proteins and the corresponding peptides,

scaling of obtained alignment hits by setting the self-alignment score of a given protein to one and aligning hits of the corresponding peptides accordingly,

counting the number of alignment hits exceeding a given threshold for each peptide,

compared the local-pairwise alignment to a randomly generated database of protein sequences with no known allergenic properties,

scaling and counting of hits,

subtracting the “non-allergic protein” counts from those of the allergen results,

calculating cumulative hit scores for each protein based on the number of hits for all corresponding peptides,

selecting proteins with highest counts as iMAT antigen module candidates.

In a specific aspect of the method step b) comprises identifying amino acid substitutions in a predetermined amino acid sequence allowing the stabilization of such predetermined amino acid sequence, preferably comprising the steps of:

(i) modeling of the three-dimensional/tertiary structure of the targeted predetermined amino acid sequence, (ii) iterative determination of protein stabilities based on single point substitutions, such as substitutions of cysteine residues with different amino acid residues, preferably serine and/or isoleucine residues, and a scoring system based on the protein stability free energy changes (ΔΔG) to determine stabilizing substitutions by analyzing all available three-dimensional/tertiary amino acid sequence structures, (iii) re-modeling of the substituted three-dimensional/tertiary amino acid sequence structure and calculation of its stability by repeating steps (ii) and (iii) until a steady state is reached.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A: shows an SDS-PAGE of MAT-Fel d1 (IVN201) under reducing conditions; FIG. 1A shows the Original SDS-PAGE (10 μg protein per lane, Coomassie staining).

FIG. 1B: shows an SDS-PAGE of MAT-Fel d1 (IVN201) under reducing conditions with bands that have been cut out of the SDS-PAGE gel shown in FIG. 1A and reloaded on SDS-PAGE (silver staining).

FIG. 2: shows an SDS-PAGE of Fel d1 under reducing conditions; NUPAGE® 4-12% Bis-Tris Gel. Lanes: 1) Marker: SeeBlue Plus2 Pre-Stained Standard 2) 5 μg Fel d1; 3) 5 μg Fel d1.

FIG. 3A: shows an RP-HPLC chromatogram 0.1% TFA/Acetonitrile gradient of native protein (MAT-Fel d1) without additives.

FIG. 3B: shows an RP-HPLC chromatogram 0.1% TFA/Acetonitrile gradient of MAT-Fel d1 denaturated by addition of guanidinium chloride plus DTT.

FIG. 4: depicts MAT-Fel d1 molecule and its Kyte Doolittle hydrophobicity plot.

FIG. 5: shows a NUPAGE® SDS-PAGE-System (4-12% Bis-Tris Gels, 1×MES-Running buffer, 35 min, 200 V). Lanes: 1) Lysozyme, 1 μg Protein ox. 2) PageRuler Prestained Protein Ladder; 3) MAT-Fel d1 (5 μg) oxidized with Iodacetamide (ox.); 4) iMAT-Cul o4 (ox.); 5) PageRuler Prestained Protein Ladder; 6) MAT-Fel d1 (5 μg) reduced; 7) iMAT-Cul o4 reduced; 8) Lysozyme reduced.

FIG. 6: shows an RP-HPLC chromatogram 0.1% TFA/Acetonitrile gradient. The peak reflects native (oxidized) protein (iMAT-Cul o4) without additives.

FIG. 7: shows the results of the following experiment: Proteins and ADJU-PHOS® that were incubated at RT for 30 min while mixing gently. After incubation, the samples were centrifuged for 3 min. and subsequently analyzed by SDS-Page Lane 1) pageRuler Prestained Protein Ladder; 2) iMAT-Cul o3 Supernatant; 3) iMAT-Cul o3 Pellet in Urea 4) iMAT-Cul o3 Supernatant; 5) iMAT-Cul o3 Pellet in Urea; 6) Empty; 7) iMAT-Cul o2 Supernatant 8) iMAT-Cul o2 Pellet in Urea 9) iMAT-Cul o2 Supernatant 10) iMAT-Cul o2 Pellet in Urea; 11) Empty; 12) iMAT-Cul o4 Supernatant; 13) iMAT-Cul o4 Pellet in Urea 14) iMAT-Cul o4 Supernatant; 15) iMAT-Cul o4 Pellet in Urea; (2, 3, 7, 8, 12, 13 w/o freeze thaw); (4, 5, 9, 10, 14, 15 after two times freeze thaw process).

FIG. 8: shows the Kyte-Doolittle hydrophobicity plot of MAT molecules versus iMAT molecules in the generic part of the respective fusion proteins [i.e. without the respective antigen module(s)]. The hydrophobicity index is shown on the Y-axis versus the amino acid position on the X-axis. Positive numbers in the index indicate hydrophobicity. The shift of the graph of the iMAT molecule at the beginning of the hydrophobicity plot as compared to the MAT molecule is due to the additional N-terminal presence of a His-tag and one methionine residue in the iMAT molecule as well as the absence of any spacer module(s).

FIG. 9A: shows examples of D. pteronyssinus allergens of the genus Dermatophagoides identifying the species, the allergen and the uniprot accession number.

FIG. 9B: shows examples of D. farinae allergens of the genus Dermatophagoides identifying the species, the allergen and the uniprot accession number.

FIG. 10: shows the N-terminus sequence alignment of invariant chains from dog and cat. The CLIP sequence is shaded in grey.

FIG. 11A: shows Histamine Release Test (Details of assay in Example 2) of 5 concentrations of iMAT-Cul o2 and the respective allergens in a polysensitized horse (Horse 1).

FIG. 11B: shows Histamine Release Test (Details of assay in Example 2) of 5 concentrations of iMAT-Cul o3 and the respective allergens in a polysensitized horse (Horse 1).

EXAMPLES

The following examples serve to further illustrate the present invention; but the same should not be construed as a limitation of the scope of the invention disclosed herein.

Example 1—Surrogate Marker for Immunity/Duration of Immunity

Administration of an (isolated) recombinant protein, as disclosed and claimed herein, to an animal, e.g. ruminants, pigs, more preferably a dog and/or a cat, but excluding an equine, produces an immunological response to the allergen and/or epitope present in the antigen module. Additionally, the C- or N-terminal tag, e.g. a HIS-tag, the TAT module together with the adjacent amino acid residues from the adjacent module is used in order to detect a unique product-specific immunological signal (e.g. an antibody—or a T-cell response) in a target subject that is used as a surrogate marker for immunity or duration of immunity. This surrogate marker, as a treatment-specific immunological parameter, enables the assessment of immunity or immune modulation or the duration of immunity or the duration of immune modulation after the administration. Thus, a specific indicator for an immune response triggered by the (isolated) recombinant protein according to the invention is the induction of terminal-tag (optionally with the adjacent amino acid residues) specific antibodies, such as IgG antibodies. Alternatively or additionally, the indicator is the induction of antibodies specific to the junction of a spacer and a module as described and claimed herein or the junction between two modules.

A single iMAT molecule such as SEQ ID NO: 57 (Der f 15 iMAT molecule (dog) with N-terminal Hexa-Histidine tag) or a combination of one or several iMAT molecules selected from SEQ ID NOs: 45, 51, 54, 57, 60, 63, 66, 69, 72 containing different antigen modules according to the present invention are employed for treating prophylactically or therapeutically a dog suffering from or being at risk of allergic diseases, especially atopic dermatitis. In such dogs the above iMAT molecules are administered as described in Example 3. In serum samples derived from a blood draw from these iMAT treated dogs, the immunological reaction upon iMAT treatment against the N-terminus of the iMAT proteins with respect to antibody production more specifically the specific IgG can be measured. The measurement employs standard ELISA (Enzyme Linked Immunosorbent Assay) techniques whereby sufficient amounts of a synthetized peptide comprising SEQ ID NO: 6 is coated on the surface of ELISA plates. Serum samples of treated animals are then incubated on such plates and the specific binding of IgG to the said peptide is detected by a secondary biotinylated antibody, specific for IgG in cats or dogs respectively, followed by application of the corresponding detection system e.g. streptavidin-peroxidase and 3,3′,5,5′-tetramethylbenzidine (TMB) as substrate.

With such ELISA test the onset of immunity elicited by iMAT immunotherapy as well as the duration of immunity is determined and observed over time. The therapeutic vaccination regime, i.e. number and schedule of booster injections, is determined by this surrogate parameter during clinical development.

Example 2—Hypoallergenicity

The allergenicity of a therapeutic allergen is of utmost importance, it is a measure of the potential to induce adverse events, e.g. provoke anaphylaxis. Exemplarily for an allergy in mammals, allergen specific IgE mediated hypersensitivity is studied in procedures as the allergen provocation tests, in particular such tests targeting the skin [Griffin C E. Diagnosis of canine atopic dermatitis DOI: 10.1002/9781118738818.ch10].

Intradermal skin tests have been used for the biological evaluation of recombinant allergens and for validation of genetically engineered hypoallergenic derivatives.

Intradermal testing in a dog is performed by administering injections of small amounts of allergen solutions directly into the dog's dermis. This is usually done with small-gauge (27 gauge) needles and injections of 0.05 to 0.1 mL at each site. The positive reactions are arbitrarily interpreted by the presence of erythema, turgidity, height, and size of the wheal.

The advantages of the intradermal tests are high sensitivities. This is of particular importance if the test shall deliver a quantitative measure for hypoallergenicity. In said tests the MAT molecules show a 10-, 100- to 1000-times or even higher molar concentration of the allergenic component as compared to the natural, native allergen applied in the same test to reach a positive reaction in sensitized individuals, as cats and dogs.

With regard to MAT molecules conflicting results about their allergenicity in comparison to the corresponding native allergens have been reported in the prior art. Senti G et al. (J Allergy Clin Immunol. 2012, 129(5): 1290-1296) demonstrated hypoallergenicity of a MAT-Fel d1 in the Cellular Antigen Stimulation Test (CAST) assay as well as in the intradermal and in the intracutaneous test. The quantitative difference in sensitivity between the allergen and the MAT molecule comprising the Fel d1 was 100-, 23- and 16-fold, respectively. Though MAT-Fel d1 was clearly hypoallergenic, some allergenicity remained. In contrast Zhao et al. Int J Clin Exp Med 2015; 8(4):6436-6443 describe their MAT-Der p1 construct to exhibit an even stronger allergenicity (hyperallergenicity) as compared to the native Der p1 protein.

Surprisingly the improved MAT molecules, as disclosed and claimed herein show clear superiority in this respect. The safety of 2 iMAT molecules manufactured according to the present invention comprising Cul o2 and Cul o3 in the antigen module, respectively, is tested. Freshly withdrawn blood of a horse sensitized to these allergens and suffering from insect bite hypersensitivity (IBH) is employed in the histamine release test (HRT) as described below.

As shown in FIG. 11B and FIG. 11A, respectively, the native allergens elicit a strong histamine release whereas surprisingly the two different iMAT molecules (iMAT-Cul o3 and iMAT-Cul o2) show virtually no response at all.

Thus, iMAT molecules show clear superiority in respect to safety as compared with the MAT molecule as described in the prior art (see above).

Histamine release test (HRT): Freshly withdrawn blood of subjects is prepared to test the basophil reactivity to (isolated) recombinant proteins/iMAT molecules, as disclosed and claimed herein. Briefly, a 10-fold dilution series (e.g. ranging from 10 nM to 0.001 nM final allergen concentration) of iMAT molecules and/or recombinant allergens is prepared in PIPES buffer (AppliChem, Darmstadt, Germany), pH 7.4. Washed red and white blood cells obtained from Na-EDTA coagulation-inhibited blood are incubated with individual dilutions for 1 h at 37° C. The reaction is stopped by incubation on ice for 20 min and the supernatant containing the released histamine is collected from each sample after centrifugation. Maximal histamine content is obtained by boiling the blood cells for 10 min in a water bath (maximal release). The incubation of releasing buffer with washed blood cells serves as a negative control (spontaneous release). Histamine concentrations are determined using a competitive RIA (LDN Nordhorn, Germany) as per the manufacturer's instructions.

Alternatively, another basophil activation test is the Cellular Antigen Stimulation Test CAST® ELISA which can also be considered as an in vitro allergy provocation test. This assay is done according to the manufacturer's instructions (Bilhlmann Laboratories AG, Allschwil, Switzerland). In the CAST®, sedimented leukocytes from allergic subjects' blood are simultaneously primed with the cytokine IL-3 and stimulated with iMAT molecules and/or recombinant allergens. Basophilic cells among others generate the allergic mediator, sulfidoleukotriene LTC4, and its metabolites LTD4 and LTE4. These freshly synthesized sulfidoleukotrienes (sLT) are subsequently measured in an ELISA test (Enzyme Linked Immunosorbent Assay).

The potential of iMAT molecules to induce adverse events, e.g. provoke anaphylaxis as a side effect of administration can be evaluated in vitro with these assays by comparing the effects of the iMAT molecules (containing an allergen) to the respective recombinant allergen alone.

A reduced basophil degranulation, e.g. histamine and/or sulfidoleukotriene release by iMAT molecules as compared to the recombinant allergen indicates a lower potential for adverse effects, i.e. a better safety profile of the iMAT molecules.

Said HRT (or CAST®) can be used as an in-vitro provocation test for type 1 allergic reactions in a subject. Allergen specific histamine release indicates the relevance of the respective allergen for the basophilic cell activation and thus can be used as a quantitative parameter for the allergen specific sensitization of a subject.

It can be expected that no allergen related adverse reactions occur if subjects suffering from allergen specific IgE mediated hypersensitivity are treated with the corresponding iMAT molecules comprising relevant allergens in the iMAT-antigen module. This makes a desensitization therapy applying iMAT proteins specifically appropriate for treatment of life threatening diseases.

The consequence of this surprising safety property of iMAT molecules in contrast to MAT molecules is, that iMAT molecules used as desensitizing proteins can be used similar to vaccines against pathogens. No up-dosing as with classical therapeutic allergens is needed, since vaccines comprising iMAT molecules do not show allergen properties with respect to allergic adverse events. Already the dose of the first injection of the iMAT molecule in a treatment course is selected based on efficacy considerations only and one does not have to consider potential allergic adverse reactions. This could not be performed using MAT molecules described in the prior art since the allergenicity of MAT, compared to the native allergen, was only reduced to a certain level. However, MAT molecules still are allergens; iMAT molecules in contrast are not. The advantage of this improved property renders a more efficacious treatment regime possible with e.g. three subcutaneous or intralymphatic injections with a high biopharmaceutical content (e.g. 3 times 1 μg to 100 μg, preferably 3 times 10 μg to 50 μg iMAT protein).

The lack of allergenicity of the iMAT molecules can be explained by the fact that in contrast to the MAT molecules described in the prior art no linker amino acid residues [i.e. spacer module(s) between the first, second and/or third module(s)] are used to separate the different modules in such iMAT molecules. It is known in the prior art that engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for the function (e.g. epitope recognition by the immune system) of the proteins [Klein J S et al., Protein Eng Des Sel. 2014, 27(10): 325-330]. The separation distance between functional units can impact epitope access and the ability to bind with avidity. If the missing amino acid residue linkers between the modules, in particular between the targeting domain and the antigen module, lead to a more rigid structure, conformational epitopes of the allergen module might not be formed due to incorrect folding. A cross linking of antibodies bound on the surface of basophils (e.g. IgE) by its high affinity receptors is necessary to induce activation and histamine release. However, misfolded allergens might not be able to induce such cross linking. Thus, an iMAT molecule without linker may not form conformational IgE epitopes which renders the iMAT molecules non-allergenic.

Example 3—Therapeutic Vaccine/Prophylaxis of Atopic Dermatitis in Dogs and/or Cats

A single iMAT molecule or a combination of iMAT molecules containing different antigen modules according to the present invention is employed for treating prophylactically or therapeutically a dog and/or a cat suffering from or to be at risk of atopic dermatitis (AD).

In first example the iMAT molecule according to SEQ ID NO: 36 (Der f 15) is administered into the popliteal lymph node of cats suffering from atopic dermatitis.

In a second example the iMAT molecule according to SEQ ID NO: 66 (Hybrid 1) is administered into the popliteal lymph node of cats suffering from atopic dermatitis.

In a third example the iMAT molecule according to SEQ ID NO: 57 (Der f 15) is administered into the popliteal lymph node of dogs suffering from atopic dermatitis.

In a fourth example the iMAT molecule according to SEQ ID NO: 81 (Hybrid 3) is administered into the popliteal lymph node of dogs suffering from atopic dermatitis.

In each case, the hair over the lymph node of the affected animal is clipped and surgically prepared. Using palpation and/or ultrasound for guidance a 25 G needle is inserted into the lymph node. The injected iMAT molecule is adsorbed to an adjuvant. The adjuvant consists e.g. of aluminum phosphate (ADJU-PHOS®, Brenntag Biosector, Denmark). The iMAT molecule stock is a frozen solution of e.g. 375 μg/mL protein concentration in vials, each containing 500 μL to be thawed before use.

After thawing the iMAT molecule solution, 400 μL of the solution are mixed with e.g. 200 μL of the adjuvant. This final formulation is left at room temperature e.g. for 60 minutes prior to the intralymphatic injection to allow for absorption of the iMAT molecule to e.g. ADJU-PHOS®, e.g. 50 μL of the mixture containing 12.5 μg iMAT molecule is removed into a 500 μL syringe for lymph node injection. This preparation is first administered typically on day 0, day 28 and day 56 in a dose between 10 μg and 50 μg (referring to the weight of solely the one or more antigen modules) per injection and iMAT molecule.

Throughout the treatment period and/or thereafter the efficacy of a therapy or the prevention of AD is investigated clinically by quantitative, semi-quantitative or qualitative assessment of pruritus, skin lesions and a medication score (Hobi S, Mueller R S; Tierarztliche Praxis. Ausgabe K, Kleintiere/Heimtiere 2014, 42(3):167-173).

These clinical parameters are compared to clinical signs of the individual dog and/or cat prior to the start of a therapeutic intervention. Alternatively, a comparison to AD affected dogs and/or cats that are not treated or treated with placebo can demonstrate the efficacy of the iMAT molecule-mediated treatment and/or prevention of clinical signs of AD.

Alternatively or in addition an intradermal provocation test with certain Dermatophagoides allergens can be employed in said dogs and/or cats. A reduced response (immediate and/or late phase reactivity) indicates a therapy and/or prevention effect of the iMAT molecule administration.

Furthermore, the modulation of the different components of the immune system are monitored, e.g. changes in allergen specific IgE and IgG antibody titers indicate therapy and/or prevention effects.

Apart from changes in IgE levels, an increase in allergen-specific IgG is surprisingly found when treating a dog and/or cat for AD with such iMAT molecules. These antibodies block IgE-mediated anaphylaxis in vivo and seem to inhibit not only the allergen-induced release of inflammatory mediators from basophils and mast cells, but also IgE-mediated allergen presentation to T cells. Among the iMAT-induced IgG antibodies specifically binding to the allergen, some allergen-specific subtypes have been suggested to play an important “protective” role, as they compete with allergen-specific IgE antibodies and can prevent the activation of CD4+ T cells, by inhibiting the IgE-mediated antigen presentation. Furthermore, the IgG subset which is secreted promotes a significant reduction in mast cells and eosinophils, accompanied by a diminished release of inflammatory mediators.

Allergen-specific immunotherapy can modulate different components of the immune system. Cellular modifications consist of a reduction in allergen-induced T-cell proliferation, indicating the induction of peripheral tolerance in allergen-specific T cells and a decrease in antigen-specific Th2-dominated immune response in favor of a Th1 reaction with increased IFN-γ production. The key cell type responsible for coordinating this immunological switch is a heterogeneous T-cell population, called regulatory T cells (T_(reg)). At the cellular level, the crucial factor for successful allergen immunotherapy is the peripheral induction of type 1 T_(reg) cells. Functional studies on type 1 T_(reg) cells, specific in recognizing antigens, revealed that the modulation of Th1 and Th2 responses by type 1 T_(reg) cells mostly depends on the secretion of the cytokine IL-10, which has immunosuppressive properties. In fact, IL-10 inhibits the proliferative response of peripheral T cells against specific allergens and plays a central role in the induction of T-cell anergy. In vitro, IL-10 enhances the expression of the regulatory factor FoxP3, modulates eosinophilic function and reduces pro-inflammatory mediators released by mast cells.

Another possible marker of the outstanding clinical efficacy of said iMAT molecules-mediated immunotherapy is the detection of changes in the number or the nature of allergen-specific T cells. On the basis of, for example, Bet v1 tetramer staining studies, the levels and characteristics of circulating birch pollen-specific CD4⁺ T cells can potentially be compared before and after SIT. Recently, transforming growth factor (TGF)-β has also been identified as a key cytokine in successful SIT. Many actions may account for its relevance, such as the suppression of specific Th1, Th2 and Th17 cells, the induction of FoxP3 and the suppressive function of Tregs. In addition, TGF-β downregulates FcεRI expression on Langerhans cells and suppresses IgE synthesis. These immunological relevant T cell mediated immunological responses can be measured in ex vivo experiments applying peripheral blood mononuclear cell (PBMC) cultures and cytokine detection thereof as described by Nuttall et al. (T. J. Nuttall et al., Veterinary immunology and Immunopathology 84 (2002) 143-150).

Example 4—Comparison of iMAT Molecules According to the Present Invention with Prior Art MAT Molecules According to WO 2004/035793 (US Equivalent US 2005/0281816)

For assessment of purity of a MAT protein, a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) test procedure has been established (Thompson J et al., J Biol Chem 2002, 277: 34310-34331). The method, including sample preparation with a reducing agent, Lithium Dodecylsulphate (LDS) and heating at 75° C., resulted in reproducible multiple sharp bands after electrophoretic separation. Staining with Coomassie blue gives linear quantitative (densitometry) features in gels loaded with 200 to 1000 ng protein. Using a monoclonal antibody, detecting the allergen module in a MAT molecule with Fel d 1 as allergen module (MAT-Fel d1) it has been shown, that the main band and 13 minor bands all contain the MAT-Fel d1 protein. The small bands migrate at the same position as on the original gel also after re-loading on the gel (FIG. 1A and FIG. 1B). Several different methods, such as different temperature and buffer composition protocols, for sample preparation prior to PAGE generated the same band pattern.

In all of these bands the presence of the full length (complete) MAT-Fel d1 protein and only traces of host cell proteins could be demonstrated after each band was cut out of the gel, digested by trypsin and subsequently analyzed by mass spectrometry (nanoLC/ESI-MS). From these experiments an anomalous feature (gel shifting), e.g. of different folding variants, of MAT-Fel d1 in the SDS-PAGE can be concluded. This means that MAT-Fel d1 in the analyzed preparation is not suitable as biopharmaceutical molecule, in particular for clinical and/or commercial biopharmaceutical manufacturing, since its purity could not be determined with standard methods (e.g. SDS-PAGE), but only with the modified procedure explained above.

In contrast to this gel shifting phenomenon of the MAT-Fel d1 molecule, the Fel d1 as such does not show such anomalous feature in SDS PAGE (FIG. 2, lanes 2 and 3). The Fel d1 displays a single sharp band at the expected molecular weight (19.6 kD).

A further anomalous feature could be observed in RP-HPLC analysis. No single peak of the MAT-Fel d1 was seen in this analytical method (FIG. 3A and FIG. 3B), neither in the native conformation of the protein (FIG. 3A) nor in the denatured form (FIG. 3B) induced by chaotropic and reducing conditions. However, for GMP certified biopharmaceutical manufacturing a single isoform of the biomolecule in marketed pharmaceutical preparations is mandatory.

These observations in SDS-PAGE and RP-HPLC analysis may be explained by the physicochemical properties based on the amino acid sequence. Analysis in the Kyte & Doolittle hydrophobicity plot [Kyte J, Doolittle R F, Journal of Molecular Biology 1982, 157(1), 105-132] revealed adjacent extreme hydrophobic and hydrophilic domains (FIG. 4) which may be responsible for this anomalous behavior.

In particular, the hydrophobic region of the targeting domain of the fusion protein is similar to the transmembrane segments of membrane proteins which are known in the art to cause such anomalous feature [Rath A et al., Proc Natl Acad Sci USA. 2009, 106(6): 1760-1765].

Migration on SDS-PAGE, which does not correlate with formula's molecular weights, termed “gel shifting” appears to be common for membrane proteins. This means, that the prerequisite of the SDS-PAGE method, which is a separation of molecules solely according to their molecular weight, independent on their native 2D- or 3D-structure does not apply in these cases. In the above cited work (PNAS article), the authors investigate the anomalous gel mobility of helical membrane proteins using a library of wild-type and mutant helix-loop-helix (“hairpin”) sequences derived from transmembrane segments 3 and 4 of the human cystic fibrosis transmembrane conductance regulator (CFTR), including disease-phenotypic residue substitutions. They found that these hairpins migrate at rates of minus 10% to plus 30% vs. their actual formula's molecular weights on SDS-PAGE and load detergent at ratios ranging from 3.4-10 g SDS/g protein. They additionally demonstrated that mutant gel shifts strongly correlate with changes in hairpin SDS loading capacity, and with hairpin helicity, indicating that gel shift behavior originates in altered detergent binding. In some cases, this differential solvation by SDS may result from replacing protein-detergent contacts with protein-protein contacts, implying that detergent binding and folding are intimately linked.

The SDS PAGE (FIG. 5) as well as the RP-HPLC analysis (FIGS. 3A, 3B, and 6) of MAT and iMAT proteins reveal substantial differences in the migration pattern or elution, respectively. The oxidized form of MAT-Fel d1 does not show a single sharp band on the SDS-PAGE gel (Lane 3) but several diffuse bands with larger and smaller apparent molecular weights than the actual 32.2 kD of MAT-Fel d1. In contrast, as an example an iMAT molecule with an antigen module of a Culicoides obsoletus allergen (iMAT-Cul o4) exhibits a single sharp band (M=41.6 kD) under oxidized conditions. Also the RP-HPLC chromatogram shows a single peak (FIG. 6).

Under reducing conditions, the MAT-Fel d1 in the SDS-PAGE reveals a main band migrating approximately at the known molecular weight but in addition some of the minor bands described in FIG. 1A and FIG. 1B known to contain the complete sequence of MAT-Fel d1 emerge again (FIG. 5, lane 6). This is an attribute, which is characteristic for the anomalous feature of MAT-Fel d1. Additionally, the RP-HPLC chromatogram of MAT-Fel d1 under reducing conditions (FIG. 3B) exhibits at least 3 different isoforms of the MAT-Fel d1. In contrast the iMAT molecules reveal characteristics evidently indicative for a single isoform in the SDS-PAGE (FIG. 5, lane 7) as well as in the RP-HPLC (FIG. 6).

The reducing conditions lead to a cleavage of the disulfide bridges in the MAT molecule, thus the MAT and the iMAT molecules should behave alike under reducing conditions if the disulphide bridges are solely responsible for the anomalous feature of MAT. However, this is not the case, since the anomalous gel shifting and the occurrence of isoforms in RP-HPLC of MAT molecules is still present under reducing conditions.

However, the iMAT molecule does not show such gel shifting and exhibits a peak in RP-HPLC chromatogram in the native (oxidized) form of the protein. Furthermore, the Kyte-Doolittle plots of MAT and iMAT molecules are nearly identical at the N-terminus covering the sequence of His-tag, TAT and targeting domain (FIG. 8). Consequently, a person skilled in the art would not be motivated to construct a MAT molecule according to the prior art with cysteine residues substituted with other amino acid residues in order to overcome the disadvantages of the prior art.

iMAT molecules can be constructed by the “bioinformatical engineering” procedures according to Example 5 below and produced by recombinant expression technology in E. coli. As an example three iMAT molecules, as shown in FIG. 7 are stable in buffer (20 mM citrate, 1 M arginine, pH 6.0) after freezing and thawing twice and could be adsorbed to ADJU-PHOS® (Brenntag, Denmark) as adjuvant, so that the iMAT molecules can be used as a vaccine. The proteins are desorbed from ADJU-PHOS® without degradation in the same buffer system (FIG. 7).

Example 5—“Bioinformatical Engineering” of iMAT Molecules: Selection of Proteins for the Antigen Module and Optimization of the Full iMAT Molecule

In order to, for example, treat dogs and/or cats with allergic disorders using the iMAT technology effectively, it is further advisable:

a) to select a protein as allergen module in iMAT molecules that is an allergen and thus has a high potential to cause hypersensitivity in affected subjects and thus can also be the target for tolerance induction, and b) to construct an iMAT molecule with said allergens that is thermodynamically stable and can be produced efficiently by protein engineering and can additionally be analyzed with standard methods to ensure sufficient enough quality (i.e. identity, purity and potency).

In order to fulfil these requirements a bioinformatics approach is chosen for the selection of the allergen to be included into the iMAT molecules according to the invention. The objective of the selection is (i) to choose one or more allergens to be expected to be of relevance in a given allergic disorder, i.e. that the majority of individuals suffering from allergic disorder are sensitized to the respective allergen, and (ii) to choose the allergen with the highest probability of comprising linear epitopes of allergen characteristics, i.e. comprising high numbers of short peptide sequences (7 to 13 amino acid residues) homologue to those in published allergens.

To select appropriate antigens for pharmaceutical preparations, a homology comparison based on local sequence alignments to known allergens is chosen. Often epitope detection for antibody recognition (mostly conformational epitopes) is achieved by functional analysis (e.g. peptide microarrays) or for T-cells epitopes (linear epitopes) by calculation of peptide binding probabilities to MHC molecules. The therapeutic principle of the iMAT technology inter alia is based on endocytosis and degradation by acid-dependent proteases in endosomes followed by MHC Class II binding and antigen presentation.

Thus a different—non experimental but bioinformatics—approach for allergen selection is chosen that is based on local homology searches of peptides derived from given proteins to known allergenic proteins, most of which are known to raise allergies in humans. Amino acid sequences of proteins suspected to have allergenic properties are exported from publicly available databases (e.g. UNIPROT) and redundancies are determined by analysis of sequences homologies within the exported dataset. Highly homologue sequence counterparts are eliminated and the resulting remainder of sequences served as the canonical sequence database of probable valid antigens for subsequent analyses. To determine proteins with putative high allergenic potential, proteins are in silico cleaved into peptides with lengths of 6 to 15 amino acids with a one amino acid shifting. Next, local-pairwise alignments of e.g. Dermatophagoides proteins and the corresponding peptides to the canonical sequence database are performed. Following this, a scaling of obtained alignment hits is conducted by setting the self-alignment score of a given protein to one and alignment hits of the corresponding peptides accordingly. Thereafter the number of alignment hits exceeding a given threshold are counted for each peptide and compared by local-pairwise alignment to a randomly generated database of protein sequences with no known allergenic properties, and subsequently scaled and counted. The resulting “non allergic protein” counts are subtracted from those of the allergen results and cumulative hit scores for each protein based on the number of hits for all corresponding peptides are calculated. Proteins with highest counts are selected as iMAT antigen module candidates.

Each of the selected allergens are integrated into separate iMAT molecules as the antigen module and subsequently the full iMAT molecule is optimized for thermodynamic stability by iterative modeling of three-dimensional protein structures and calculation of changes of free energies after substitution of single amino acids. Physicochemical properties and stability is influenced by substituting different amino acid residue(s) within the primary amino acid sequence.

The results of the herein described analyses (antigen search and modeling) are transformed into an iMAT amino acid sequence suitable for pharmacological production and application.

In a specific example, this bioinformatics engineering approach identifies Zen 1 and Der f 15 to be of relevance in the allergic disorder atopic dermatitis elicited by proteins derived from the mite species Dermatophagoides farinae. Furthermore, the bioinformatics analysis reveals stable iMAT molecules with cysteines substituted by other amino acid residues. Examples of such stable iMAT molecules are SEQ ID NO: 39 (Dog Zen1) and SEQ ID NO: 57 (Dog Der f 15).

Example 6—Construction of Mosaic-Like iMAT Molecules According to the Invention

It is expected that iMAT molecules according to the invention is further improved if components of more than one allergen are included into the antigen module. For this purpose, it is possible to apply the basic principle of the above described bioinformatics selection approach (Example 5) in a different way. Instead of selecting complete allergens based on the hit count of allergen peptides found in the allergen data base, only the most abundant peptides of several of such allergens are used to engineer an iMAT antigen module. Thus, such an iMAT molecule consists of an antigen module of peptides that stem from several allergens. This allows broadening of the spectrum of a single iMAT molecule with respect to its targeted allergic profile and is thus beneficial for pharmacological drug development.

In order to find short peptide sequences that qualify for such mosaic-like iMAT molecule proteins from e.g. Dermatophagoides are analyzed by homology comparison as described above. Briefly in silico cleaved proteins with peptide lengths of 6-15 amino acid residues are locally aligned to a canonical sequence database of allergen-related proteins and a random database of non-allergy-related proteins. The number of differences of significant homologies for each peptide found within the canonical database is determined. Subsequently, each peptide is locally aligned to a random database triple the size of the canonical database to reduce false positive hits. The top (e.g. tenth percentile) of remaining homologies for each peptide length is especially suitable to serve as a base for construction of a mosaic-like or hybrid allergen carrying iMAT molecule. To construct a mosaic-like iMAT molecule a protein precursor is chosen (for example from the list of precursor proteins corresponding to top ranking peptides) as a scaffold protein for embedding top ranking peptides. The signal peptide sequence is removed from the scaffold protein and top ranking peptides, optionally with additional adjacent N- or C-terminal amino acids, can be inserted within the original sequence of the scaffold protein or can replace parts of the original sequence of the scaffold protein. The position for insertion or replacement is determined using similarity alignments or the reference position of the peptide in the corresponding precursor protein. As a next step, His-Tag, the TAT and targeting domain are added. Finally, cysteine residues are replaced by most stabilizing residues as described above.

In a specific example (hybrid 1), this bioinformatics engineering approach identifies a combination of SEQ ID NO: 84 (A1KXC1_DERFA DFP1 OS=Dermatophagoides farinae), SEQ ID NO: 10 (Q86R84_DERFA 60 kDa allergen Der f 18p OS=Dermatophagoides farinae GN=Der f 18 PE=2 SV=1), SEQ ID NO: 85 (A0A088SAS1_DERFA Der f 28 allergen OS=Dermatophagoides farinae PE=2 SV=1), SEQ ID NO: 88: (A7XXV2_DERFA Der f 2 allergen OS=Dermatophagoides farinae PE=4 SV=1), SEQ ID NO: 86 (B7U5T1_DERFA Der f 6 allergen OS=Dermatophagoides farinae PE=2 SV=1), SEQ ID NO: 87 (T2B4F3_DERPT LytFM OS=Dermatophagoides pteronyssinus GN=lytFM PE=4 SV=1), SEQ ID NO: 11 (Q9U6R7_DERFA 98 kDa HDM allergen OS=Dermatophagoides farinae PE=2 SV=1)

to be of relevance in the allergic disorder atopic dermatitis elicited by proteins derived from the mite species Dermatophagoides farinae. Furthermore, the bioinformatics analysis reveals stable iMAT molecules with cysteines substituted by other amino acid residues. Examples of such stable mosaic-like iMAT molecules are

SEQ ID NOS: 75 (Dog Hybrid 1) and SEQ ID NO: 66 (Cat Hybrid 1).

Example 7—Therapeutic Vaccine/Prophylaxis of Allergic Asthma in Cats

A single iMAT molecule or a combination of iMAT molecules containing different antigen modules according to the present invention can be employed for treating prophylactically or therapeutically a cat suffering from or being at risk of allergic asthma. In cats iMAT molecules according to the present invention are administered as described in Example 3.

Adult cats with a known history of allergic asthma will be included in the study, i.e. cats reported to exhibit clinical signs as spastic coughing episodes, wheezing and expiratory dyspnea.

Bronchioalveolar lavage fluids (BALF) are collected prior to treatment start and e.g. 2, 3, and 6 months during/after treatment. BALF is used for cytologic examination and nucleated cell counts.

Cats are sedated with e.g. Ketamine HCl intravenously. Bronchoalveolar lavage fluid is collected by gently inserting e.g. a 7 Fr polypropylene catheter through the endotracheal tube. When resistance is felt, an up to 20 ml aliquot of warmed sterile saline is lavaged through the catheter and retrieved by manual suction. After centrifugation and resuspension, a smear cytology of the collected BALF cells is prepared, the presence of significant numbers of eosinophils support a diagnosis of feline asthma. Differential cell counts can quantitatively evaluate the ratio (%) of eosinophils in BAL fluids.

Alternatively or in addition, employing certain recombinant allergens an intradermal provocation test, skin prick test or also allergen specific IgE and/or IgG determination in BAL fluid or serum can be monitored in said cats (Norris et al., Vet Immunol Immunopathol. 2003, 96(3-4): 119-127). A reduced response (immediate and/or late phase reactivity) and/or changes of the antibody titers indicate a therapy and/or prevention effects of the iMAT molecule treatment.

Clinical signs as the respiratory rate and scores to account for respiratory effort/difficulty are employed. Said “respiratory scoring system” can be employed also e.g. in response to an aerosol challenge. Briefly, awake, spontaneously breathing cats in a sealed chamber are exposed for different time length and/or different concentrations of aerosolized recombinant allergens. Alternatively, quantitative measures of the airway hyper-responsiveness can be performed in anesthetized cats. Pneumotachograph measurements can be done baseline and in a broncho-provocation protocol e.g. a dose response of the pulmonary resistance to methacholine and/or selected recombinant allergens.

Thus, throughout the treatment period and/or thereafter the efficacy of a therapy or the prevention of allergic asthma is investigated clinically by quantitative, semi-quantitative or qualitative assessments.

The parameters can be compared in the individual cat to the severity prior to the start of a therapeutic intervention. Alternatively, a comparison to cats with allergic asthma that are not treated or treated with placebo demonstrates the efficacy of the iMAT molecule-mediated treatment and/or prevention of clinical signs of feline allergic asthma.

Example 8—Therapeutic Vaccine/Prophylaxis of Flea Allergy in Cats and/or Dogs

A single iMAT molecule or a combination of iMAT molecules containing different antigen modules according to the present invention can be employed for treating prophylactically or therapeutically a cat and/or a dog suffering from or being at risk of flea atopic dermatitis.

In a first example the iMAT molecule according to SEQ ID NO: 42 (Cat Cte f 1) is administered into the popliteal lymph node of cats suffering from or being at risk of flea atopic dermatitis.

In a second example the iMAT molecule according to SEQ ID NO: 63 (Dog Cte f 1) is administered into the popliteal lymph node of dogs suffering from or being at risk of flea atopic dermatitis.

The further treatment details are as described in Example 3 above.

The efficacy of said iMAT treatment is evaluated by an intradermal test (IDT), T-cell analyses and measurement of flea allergen specific IgE and IgG (Gerber, J. D. Vaccine 1990-12-8(6):536-542) in treated cats and/or dogs before and after iMAT treatment as described by Jin (Jin J et al., Vaccine 28 (2010) 1997-2004). Intradermal tests (IDTs) are done following the protocol from Hillier and DeBoer, (DeBoer, D. J., Hillier, A. Veterinary Immunology and Immunopathology 2001, 81 (3-4), 271-276). 4 weeks after the last immunization, the cats and/or dogs are injected with 100 μl PBS containing 100 μg of flea extract on the lateral thorax skin of the cats and/or dogs intradermally; histamine is used as positive control, BSA used as an irrelevant stimulator, and saline used as the negative control. The size of reactive bleb on the skin is marked with a marker pen and measured perpendicularly and horizontally within 20 min after the challenge by a micrometer. The results are calculated as an average of the three measurements. A reduced response (immediate and/or late phase reactivity) and/or changes of the antibody titers or Th1 or Treg skewed T-cell responses indicate a therapy and/or prevention effects of the iMAT molecule treatment.

REFERENCES

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1. An improved MAT (iMAT) molecule, comprising: (i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, and (iii) at least one third module as antigen module being an amino acid sequence derived from at least one epitope of at least one antigen, determining the specificity of an immune response modulated by such iMAT molecule, wherein in the entire iMAT molecule all cysteine residues are substituted with a different amino acid residue, wherein the at least one second module is selected from the group consisting of: the invariant chain selected from the canine and/or feline species' or a partial sequence thereof, and wherein the at least one antigen module comprises at least one epitope derived from at least one allergen eliciting an immune response in animals is selected from members of the genus Canis or Felis, in response to flea bites, allergens derived from fleas and/or mites food allergies, atopic dermatitis, atopic dermatitis caused by flea bites, allergic asthma, allergic airway inflammation and/or obstruction.
 2. (canceled)
 3. The iMAT molecule according to claim 1, wherein the modules are covalently linked to each other, and wherein no additional spacer module(s) between two or more adjacent modules of said first, second, and/or third modules are present.
 4. The iMAT molecule according to claim 1, wherein the at least one second module comprises, one or more of the amino acid sequences of SEQ ID NO: 4 (canine) or SEQ ID NO: 5 (feline) or fragments thereof. 5-7. (canceled)
 8. The iMAT molecule according to claim 1, wherein said at least one allergen comprises Der f 15 allergen according to SEQ ID NO: 11 and/or 18, and/or Cte f1 allergen according to SEQ ID NO: 13 and/or
 20. 9. (canceled)
 10. The iMAT molecule according to claim 1, further comprising at least one tag module, wherein said at least one tag module is present N-terminally and/or C-terminally.
 11. (canceled)
 12. The iMAT molecule according to claim 10, wherein said at least one tag module is a His-tag module which is present N-terminally after one methionine residue.
 13. The iMAT molecule according to claim 1, wherein the at least one first module comprises the amino acid sequence of HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof.
 14. The iMAT molecule according to claim 13, wherein, such at least one first module comprises SEQ ID NO:
 1. 15. The iMAT molecule according to claim 1, wherein the third module comprises any one of SEQ ID NOs: 14 to
 23. 16. The iMAT molecule according to claim 1, comprising any one of SEQ ID NOS: 24 to
 83. 17-18. (canceled)
 19. An amino acid sequence of an improved MAT (iMAT) molecule, comprising: (i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, and (iii) at least one third module as antigen module being an amino acid sequence derived from at least one epitope of at least one antigen, determining the specificity of an immune response modulated by such iMAT molecule, wherein said first module comprises SEQ ID NO. 1, wherein the second module consists of SEQ ID NOs: 4 or 5, and wherein the third module consists of any one of SEQ ID NOs: 14 to
 23. 20-22. (canceled)
 23. The amino acid sequence according to claim 19, wherein the third module comprises SEQ ID NO:
 18. 24. The amino acid sequence according to claim 19, wherein the modules are covalently linked to each other, and wherein no additional spacer module(s) between two or more adjacent modules of such first, second and/or third modules are present at all.
 25. The amino acid sequence according to claim 19, further comprising at least one His-tag module, wherein said Hid-tag module is present N-terminally and/or C-terminally.
 26. (canceled)
 27. The amino acid sequence according to claim 25, wherein said at least one His-tag module is present N-terminally after one methionine residue.
 28. The amino acid sequence according to claim 19, wherein said amino acid sequence comprises any one of SEQ ID NOs: 24-83. 29-31. (canceled)
 32. The amino acid sequence according to claim 28, wherein said amino acid sequence comprises SEQ ID NO: 36 (Der f15 iMAT molecule cat), SEQ ID NO: 37 (Der f15 iMAT molecule cat), SEQ ID NO: 38 (Der f15 iMAT molecule cat), SEQ ID NO: 57 (Der f15 iMAT molecule dog), SEQ ID NO: 58 (Der f15 iMAT molecule dog), or SEQ ID NO: 59 (Der f15 iMAT molecule dog).
 33. The amino acid sequence according to claim 28, wherein said amino acid sequence/iMAT molecule comprises SEQ ID NO: 68 or SEQ ID NO:
 77. 34. An amino acid sequence, comprising: (i) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, comprising SEQ ID NO: 1, (ii) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, comprising SEQ ID NO: 4 or 5, and (iii) at least one third module as antigen module being an amino acid sequence derived from at least one full or partial amino acid sequence of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 9, 10, 11, 12, 84, 85, 86, 87, and 88, determining the specificity of an immune response modulated by such iMAT molecule, wherein at least in the antigen modules all cysteine residue are substituted with a different amino acid residue.
 35. The amino acid sequence/improved MAT (iMAT) molecule according to claim 34, wherein the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 10, 11, 84, 85, 86, 87, and 88 (Hybrid 1), or wherein the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 9,10, 11, and 12 (Hybrid 2) or wherein the antigen module is an amino acid sequence derived from at least one full or partial amino acid sequence of any combination of two or more antigens selected from the group consisting of: SEQ ID NO: 7, 8, 10, and 11 (Hybrid 3).
 36. The amino acid sequence according to claim 35, wherein the antigen module is an amino acid sequence based on a backbone derived from SEQ ID NO: 84 comprising any combination of one or more of the peptides according to SEQ ID NOs: 91-96 embedded into said backbone sequence, or wherein the antigen module is an amino acid sequence derived from any combination of two or more of the peptides according to SEQ ID NOs: 97-102, or wherein the antigen module is an amino acid sequence derived from any combination of two or more of the peptides according to SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 101, and SEQ ID NO:
 102. 37. An amino acid sequence comprising any of SEQ ID NO: 36 (Der f15 iMAT molecule cat), SEQ ID NO: 37 (Der f15 iMAT molecule cat), SEQ ID NO: 38 (Der f15 iMAT molecule cat), SEQ ID NO: 57 (Der f15 iMAT molecule dog), SEQ ID NO: 58 (Der f15 iMAT molecule dog), SEQ ID NO: 59 (Der f15 iMAT molecule dog), SEQ ID NO: 66 (hybrid 1 iMAT cat), SEQ ID NO: 67 (hybrid 1 iMAT cat), SEQ ID NO: 68 (hybrid 1 iMAT cat), SEQ ID NO: 75 (hybrid 1 iMAT dog), SEQ ID NO: 76 (hybrid 1 iMAT dog) and/or SEQ ID NO: 77 (hybrid 1 iMAT dog). 38-42. (canceled) 